Injection Sites and Stereotaxic Coordinates
Transcription
Injection Sites and Stereotaxic Coordinates
Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER: INJECTION SITES AND STEREOTAXIC COORDINATES FOR ANTEROGRADE PROJECTOME (BRAIN-WIDE) Table 1. Stereotaxic coordinates used for axonal projection mapping study (excluding ISI-directed visual area injections). Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Abducens nucleus VI Chat-IRES-Cre 168616111 -5.52 0.50 3.75 0 Accessory olfactory bulb AOB C57BL/6J 120812686 3.20 1.00 1.40 0 Accessory olfactory bulb AOB C57BL/6J 272918345 3.70 1.50 0.40 0 Accessory olfactory bulb AOB Cdhr1-Cre_KG66 182686228 3.08 1.00 1.75 0 Accessory olfactory bulb AOB Efr3aCre_NO108 267760731 2.80 1.25 1.30, 1.67 0 Accessory olfactory bulb AOB Gad2-IRES-Cre 266563321 3.08 1.00 1.75 0 Accessory olfactory bulb AOB Syt17-Cre_NO14 161178152 3.00 1.00 1.50 0 Agranular insular area AI C57BL/6J 112596790 1.78 2.40, 2.80 2.24 0 Agranular insular area AI Chrna2Cre_OE25 292209592 1.78 2.40, 2.80 2.25 0 Agranular insular area AI Cux2-IRES-Cre 299783689 1.10 3.25 1.9, 2.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 1 of 117 Experiment ID AP ML DV Angle° alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Agranular insular area AI Htr2aCre_KM207 262536037 1.78 2.40, 2.80 2.25 0 Agranular insular area AI Rbp4-Cre_KL100 296048512 1.78 2.40, 2.80 2.25 0 Agranular insular area, dorsal part AId A930038C07RikTg1-Cre 267397941 1.78 2.40, 2.80 2.24 0 Agranular insular area, dorsal part AId C57BL/6J 170721670 3.10 1.40 0.65 0 Agranular insular area, dorsal part AId C57BL/6J 180673746 3.10 1.40 0.65 0 Agranular insular area, dorsal part AId C57BL/6J 180709230 2.60 2.00 2.40 0 Agranular insular area, dorsal part AId Glt25d2Cre_NF107 313327028 1.78 2.40 2.25 0 Agranular insular area, dorsal part AId Grp-Cre_KH288 184168899 1.78 2.80 2.25 0 Agranular insular area, dorsal part AId Ntsr1Cre_GN220 159322514 1.78 2.40, 2.80 2.24 0 Agranular insular area, dorsal part AId Rbp4-Cre_KL100 166153483 1.78 2.40, 2.80 2.24 0 Agranular insular area, dorsal part AId Syt6-Cre_KI148 264320859 1.78 2.40, 2.80 2.24 0 Agranular insular area, dorsal part AId Tlx3-Cre_PL56 294525229 -4.36 4.25 1.35 0 Agranular insular area, posterior part AIp C57BL/6J 174361746 -0.58 4.00 2.15 0 Agranular insular area, posterior part AIp Chrna2Cre_OE25 297858011 -0.34 3.85 3.00 0 Agranular insular area, posterior part AIp Cux2-IRES-Cre 272827141 -0.34 4.00, 3.75 3.00 0 Agranular insular area, posterior part AIp Rbp4-Cre_KL100 183330908 -0.34 4.00, 3.75 3.00, 3.25 0 Agranular insular area, posterior part AIp Syt6-Cre_KI148 168095756 -0.34 4.00, 3.75 3.00, 3.25 0 Anterior amygdalar area AAA Adcyap1-2A-Cre 187269162 -0.46 2.20 5.22 0 Anterior amygdalar area AAA C57BL/6J 159650350 0.14 2.10 4.80 0 Anterior amygdalar area AAA C57BL/6J 175372863 -0.30 2.12 4.95 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 2 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterior amygdalar area AAA Gad2-IRES-Cre 299245589 -0.30 2.00 4.85 0 Anterior amygdalar area AAA Rbp4-Cre_KL100 300641829 -0.46 2.20 5.22 0 Anterior cingulate area ACA Efr3aCre_NO108 267749107 0.26 0.25 1.25 0 Anterior cingulate area ACA Gpr26Cre_KO250 265712971 0.26 0.25 1.25 0 Anterior cingulate area ACA Gpr26Cre_KO250 287248684 1.10 0.25 0.85 0 Anterior cingulate area ACA Grp-Cre_KH288 265291552 0.26 0.25 1.25 0 Anterior cingulate area ACA Htr2aCre_KM207 287714903 1.10 0.25 1.30 0 Anterior cingulate area ACA Ntsr1Cre_GN220 266412788 0.26 0.50 1.43 0 Anterior cingulate area ACA Scnn1a-Tg3-Cre 268038262 0.26 0.25 1.25 0 Anterior cingulate area ACA Syt6-Cre_KI148 299829892 1.10 0.25 1.30 0 Anterior cingulate area, dorsal part ACAd A930038C07RikTg1-Cre 166323896 1.10 0.25 1.00 0 Anterior cingulate area, dorsal part ACAd A930038C07RikTg1-Cre 171275617 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd A930038C07RikTg1-Cre 286774770 1.00 0.75 0.30, 0.75 0 Anterior cingulate area, dorsal part ACAd C57BL/6J 112458114 1.10 0.25 1.00 0 Anterior cingulate area, dorsal part ACAd C57BL/6J 139426984 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd C57BL/6J 146593590 0.14 0.70 0.40, 0.80 0 Anterior cingulate area, dorsal part ACAd Calb2-IRES-Cre 175719341 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Chrna2Cre_OE25 278069982 0.26 0.27 0.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 3 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterior cingulate area, dorsal part ACAd Chrna2Cre_OE25 292125472 1.10 0.25 0.85 0 Anterior cingulate area, dorsal part ACAd Cort-T2A-Cre 165644051 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Crh-IRES-Cre (BL) 183104511 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Cux2-IRES-Cre 182338356 1.10 0.25 0.85 0 Anterior cingulate area, dorsal part ACAd Cux2-IRES-Cre 183461297 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Efr3aCre_NO108 267705378 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Efr3aCre_NO108 277908168 1.10 0.25 0.85 0 Anterior cingulate area, dorsal part ACAd Erbb4-2ACreERT2 156742543 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Erbb4-2ACreERT2 182183683 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Etv1-CreERT2 114428632 1.10 0.25 1.00 0 Anterior cingulate area, dorsal part ACAd Etv1-CreERT2 181858761 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Gad2-IRES-Cre 167512351 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Gng7-Cre_KH71 158018630 0.25 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Grp-Cre_KH288 183472596 1.10 0.25 0.85 0 Anterior cingulate area, dorsal part ACAd Grp-Cre_KH288 184169615 2.10 0.75 0.35, 0.75 0 Anterior cingulate area, dorsal part ACAd Htr2aCre_KM207 183618139 2.10 0.75 0.35, 0.75 0 Anterior cingulate area, dorsal part ACAd Htr3aCre_NO152 305525773 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Ntsr1Cre_GN220 181179335 0.26 0.50 0.95 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 4 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterior cingulate area, dorsal part ACAd Ntsr1Cre_GN220 266964075 2.10 0.75 0.35, 0.75 0 Anterior cingulate area, dorsal part ACAd Pvalb-IRES-Cre 168401109 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Rbp4-Cre_KL100 125833030 0.26 0.27 0.80 0 Anterior cingulate area, dorsal part ACAd Rbp4-Cre_KL100 161458737 1.10 0.25 1.00 0 Anterior cingulate area, dorsal part ACAd Scnn1a-Tg3-Cre 267101850 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Scnn1a-Tg3-Cre 268039675 1.10 0.25 0.85 0 Anterior cingulate area, dorsal part ACAd Sst-IRES-Cre 288262635 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Syt6-Cre_KI148 177783204 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Tac1-IRES2-Cre 286646877 0.26 0.27 0.60 0 Anterior cingulate area, dorsal part ACAd Trib2-2ACreERT2 287599685 0.26 0.27 0.60 0 Anterior cingulate area, ventral part ACAv A930038C07RikTg1-Cre 159319654 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv A930038C07RikTg1-Cre 298797288 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv C57BL/6J 112514202 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv C57BL/6J 139520203 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Chrna2Cre_OE25 278173743 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Chrna2Cre_OE25 299782983 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv Cux2-IRES-Cre 183470468 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Efr3aCre_NO108 301179679 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv Etv1-CreERT2 114475228 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Grp-Cre_KH288 184213701 1.10 0.25 1.30 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 5 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterior cingulate area, ventral part ACAv Grp-Cre_KH288 265288825 1.34 1.50 0.35, 0.75 0 Anterior cingulate area, ventral part ACAv Ntsr1Cre_GN220 156546627 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Rasgrf2-2A-dCre 303783015 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Rbp4-Cre_KL100 126117554 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Rbp4-Cre_KL100 286482701 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv Scnn1a-Tg3-Cre 278502708 1.10 0.25 1.30 0 Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 125801033 0.26 0.25 1.25 0 Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 126190033 0.26 0.27 0.80 0 Anterior cingulate area, ventral part ACAv Syt6-Cre_KI148 156785529 1.10 0.25 1.00 0 Anterior cingulate area, ventral part ACAv Trib2-2ACreERT2 287600392 0.26 0.25 1.25 0 Anterior hypothalamic nucleus AHN C57BL/6J 127649713 -0.34 3.00 5.52 30 Anterior hypothalamic nucleus AHN C57BL/6J 127649713 -0.34 3.00 5.52 30 Anterior hypothalamic nucleus AHN C57BL/6J 180674463 -0.58 0.20 4.75 0 Anterior hypothalamic nucleus AHN C57BL/6J 181057754 -0.70 0.40 5.46 0 Anterior hypothalamic nucleus AHN Gad2-IRES-Cre 266490034 -0.46 0.50 4.80 0 Anterior hypothalamic nucleus AHN Gad2-IRES-Cre 300167479 -0.70 0.37 5.50 0 Anterior hypothalamic nucleus AHN Gnrh1-Cre 160399309 0.02 0.25 4.90 0 Anterior hypothalamic nucleus AHN Htr3aCre_NO152 305677409 -0.46 1.00 4.88 0 Anterior hypothalamic nucleus AHN Lypd6Cre_KL156 298049545 -0.46 0.50 5.30 0 Anterior hypothalamic nucleus AHN Sim1-Cre 159375743 -0.46 0.50 4.94 0 Anterior hypothalamic nucleus AHN Sim1-Cre 182842391 -0.58 0.20 4.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 6 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterior hypothalamic nucleus AHN Slc17a6-IRESCre 292035484 -0.46 0.50 4.80 0 Anterior hypothalamic nucleus AHN Slc18a2Cre_OZ14 301673462 -0.58 0.20 4.75 0 Anterior olfactory nucleus AON C57BL/6J 113443572 2.96 1.14 2.60 0 Anterior olfactory nucleus AON C57BL/6J 121509711 2.80 0.75 2.60 0 Anterior olfactory nucleus AON Chrna2Cre_OE25 304719312 2.80 0.75 2.60 0 Anterior olfactory nucleus AON Htr2aCre_KM207 287715650 3.08 1.00 3.42 0 Anterior olfactory nucleus AON Slc17a6-IRESCre 293546902 3.08 1.00 1.85 0 Anterior olfactory nucleus AON Slc17a7-IRES2Cre 267103498 2.96 1.14 2.60 0 Anterior olfactory nucleus AON Syt17-Cre_NO14 159994059 2.96 1.14 2.66 0 Anterior olfactory nucleus AON Syt17-Cre_NO14 159994767 2.80 0.75 2.60 0 Anterior olfactory nucleus AON Syt17-Cre_NO14 170949055 2.80 0.75 2.60 0 Anterior olfactory nucleus AON Tac1-IRES2-Cre 294313246 2.96 1.14 2.60 0 Anterior pretectal nucleus APN C57BL/6J 125363160 -2.30 0.80 3.20 0 Anterior pretectal nucleus APN C57BL/6J 127083591 -2.92 1.25 2.76 0 Anterior pretectal nucleus APN C57BL/6J 147789031 -2.80 1.00 2.15 0 Anterior pretectal nucleus APN Efr3aCre_NO108 299759175 -3.16 1.60 2.85 0 Anterior pretectal nucleus APN Gad2-IRES-Cre 305235787 -2.70 1.20 2.92 0 Anterior pretectal nucleus APN Grp-Cre_KH288 265293391 -2.92 1.25 2.76 0 Anterior pretectal nucleus APN Slc32a1-IRESCre 264076081 -0.70 2.70 2.39 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 7 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anterodorsal nucleus AD Slc6a5Cre_KF109 155735826 -0.70 0.60 2.90 0 Anterodorsal nucleus AD Slc6a5Cre_KF109 182280916 -0.70 0.60 2.90 0 Anterolateral visual area VISal A930038C07RikTg1-Cre 283017324 -3.40 3.60 0.45 0 Anterolateral visual area VISal C57BL/6J 116903968 -3.40 3.50 0.45 0 Anterolateral visual area VISal C57BL/6J 120437703 -3.08 4.00 0.80 0 Anterolateral visual area VISal C57BL/6J 146858755 -3.40 3.50 0.45 0 Anterolateral visual area VISal Chrna2Cre_OE25 292174264 -4.16 3.95 0.85 0 Anterolateral visual area VISal Cux2-IRES-Cre 266487079 -3.40 3.60 0.45 0 Anterolateral visual area VISal Cux2-IRES-Cre 287495026 1.70 0.40 2.00 0 Anterolateral visual area VISal Gpr26Cre_KO250 301210923 -3.40 3.60 0.45 0 Anterolateral visual area VISal Nr5a1-Cre 277849965 -3.40 3.60 0.45 0 Anterolateral visual area VISal Ntsr1Cre_GN220 287036898 -3.40 3.60 0.45 0 Anterolateral visual area VISal Rbp4-Cre_KL100 167794131 -3.40 3.50 0.45 0 Anterolateral visual area VISal Rorb-IRES2-Cre 298757426 -3.40 3.60 0.45 0 Anterolateral visual area VISal Scnn1a-Tg3-Cre 166459778 -3.40 3.50 0.45 0 Anterolateral visual area VISal Syt6-Cre_KI148 159224478 -3.40 3.50 0.45 0 Anterolateral visual area VISal Syt6-Cre_KI148 292791310 -4.04 4.00 0.35, 0.75 30 Anterolateral visual area VISal Tlx3-Cre_PL56 297225422 -4.04 4.00 0.35, 0.75 30 Anterolateral visual area VISal Tlx3-Cre_PL56 297231636 -3.40 3.60 0.45 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 8 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anteromedial nucleus AM C57BL/6J 146658170 -0.46 0.50 3.43 0 Anteromedial nucleus AM C57BL/6J 158840459 -0.34 0.35 3.58 0 Anteromedial nucleus AM Cck-IRES-Cre 159331462 -0.34 0.35 3.58 0 Anteromedial nucleus AM Crh-IRES-Cre (ZJH) 171067319 -0.10 2.55 4.00 30 Anteromedial nucleus AM Grik4-Cre 167571459 -0.58 0.50 3.43 0 Anteromedial nucleus AM Prkcd-GluClaCFP-IRES-Cre 267610466 -0.58 0.50 3.43 0 Anteromedial nucleus, dorsal part AMd C57BL/6J 146046430 -0.70 0.60 2.90 0 Anteromedial nucleus, dorsal part AMd Gal-Cre_KI87 266174045 -0.58 0.50 3.43 0 Anteromedial visual area VISam A930038C07RikTg1-Cre 298324391 -3.16 1.55 0.17, 0.58 0 Anteromedial visual area VISam C57BL/6J 100141599 -3.16 1.55 0.17, 0.58 0 Anteromedial visual area VISam C57BL/6J 146077302 3.08 1.50 0.40 0 Anteromedial visual area VISam Chrna2Cre_OE25 297946154 -4.60 3.80 0.45 30 Anteromedial visual area VISam Cux2-IRES-Cre 263780729 -3.80 2.50 0.35 0 Anteromedial visual area VISam Drd3-Cre_KI196 297670312 -2.54 1.75 0.20, 0.55 0 Anteromedial visual area VISam Nos1-CreERT2 308385516 -3.80 2.50 0.35, 0.75 0 Anteromedial visual area VISam Rbp4-Cre_KL100 159753308 -2.54 1.75 0.20, 0.55 0 Anteromedial visual area VISam Rbp4-Cre_KL100 286418177 -3.16 1.55 0.17, 0.58 0 Anteromedial visual area VISam Rbp4-Cre_KL100 294481346 -3.16 1.55 0.17, 0.58 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 9 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Anteromedial visual area VISam Rorb-IRES2-Cre 301618122 -3.16 1.55 0.17; 0.58 0 Anteromedial visual area VISam Scnn1a-Tg3-Cre 257667830 -3.16 1.55 0.17, 0.58 0 Anteromedial visual area VISam Syt6-Cre_KI148 299733445 -3.16 1.55 0.17, 0.58 0 Anteroventral nucleus of thalamus AV C57BL/6J 114427219 -0.58 1.00 2.93 0 Anteroventral nucleus of thalamus AV Gal-Cre_KI87 175818392 -0.58 1.00 2.93 0 Anteroventral nucleus of thalamus AV Gpr26Cre_KO250 286553311 -0.58 1.00 2.93 0 Anteroventral nucleus of thalamus AV Grp-Cre_KH288 292478008 -0.58 1.00 2.93 0 Anteroventral nucleus of thalamus AV Slc17a6-IRESCre 309702727 -0.82 1.13 3.28 0 Anteroventral periventricular nucleus AVPV C57BL/6J 138059031 0.98 0.25 4.80 0 Anteroventral periventricular nucleus AVPV Kiss1-Cre 299247009 0.50 0.15 4.75 0 Arcuate hypothalamic nucleus ARH Agrp-IRES-Cre 146554676 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Agrp-IRES-Cre 146660999 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Erbb4-2ACreERT2 277854208 -1.22 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Erbb4-2ACreERT2 306271212 -1.70 0.20 5.90 0 Arcuate hypothalamic nucleus ARH Gal-Cre_KI87 176431817 -1.22 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Gal-Cre_KI87 178282527 -1.70 0.20 5.90 0 Arcuate hypothalamic nucleus ARH Ins2-Cre 286318327 -1.22 0.15 5.45 0 Arcuate hypothalamic nucleus ARH Ins2-Cre 298105299 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Kiss1-Cre 232310521 -1.22 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Kiss1-Cre 232311236 -1.70 0.20 5.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 10 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Arcuate hypothalamic nucleus ARH Lepr-IRES-Cre 171482142 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Lepr-IRES-Cre 181891892 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Pomc-Cre (BL) 175738378 -1.70 0.20 5.90 0 Arcuate hypothalamic nucleus ARH Pomc-Cre (BL) 263369222 -1.22 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Pomc-Cre (ST) 158142090 -1.46 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Pomc-Cre (ST) 159751184 -1.90 0.25 5.40 0 Arcuate hypothalamic nucleus ARH Slc32a1-IRESCre 266489212 -1.22 0.10 5.90 0 Arcuate hypothalamic nucleus ARH Tac2-IRES2-Cre 241278553 -1.70 0.20 5.90 0 Arcuate hypothalamic nucleus ARH Th-Cre_FI172 286726777 -1.22 0.10 5.90 0 Auditory areas AUD C57BL/6J 116903230 -2.54 4.20 1.25 0 Auditory areas AUD Rasgrf2-2A-dCre 298719484 -2.46 4.35 0.85 0 Barrington's nucleus B Chat-IRES-Cre 267151656 -5.30 0.80 2.75 0 Basolateral amygdalar nucleus, anterior part BLAa C57BL/6J 113144533 -1.06 3.00 3.90 0 Basolateral amygdalar nucleus, anterior part BLAa C57BL/6J 277710753 -0.70 3.00 4.35 0 Basolateral amygdalar nucleus, ventral part BLAv Slc32a1-IRESCre 305321177 -1.70 2.75 5.25 0 Basomedial amygdalar nucleus BMA C57BL/6J 273028004 -1.06 2.75 5.40 0 Basomedial amygdalar nucleus BMA Erbb4-2ACreERT2 165972951 -0.94 2.60 4.60 0 Basomedial amygdalar nucleus, posterior part BMAp C57BL/6J 113935990 -1.06 2.50 4.84 0 Basomedial amygdalar nucleus, posterior part BMAp C57BL/6J 125832322 -1.82 3.25 4.25 10 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 11 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Basomedial amygdalar nucleus, posterior part BMAp Rbp4-Cre_KL100 182294687 -1.70 2.75 5.25 0 Bed nuclei of the stria terminalis BST C57BL/6J 117312486 0.38 0.50 3.90 0 Bed nuclei of the stria terminalis BST C57BL/6J 146747721 0.62 1.20 4.84 0 Bed nuclei of the stria terminalis BST C57BL/6J 147049515 0.02 0.50 3.58 0 Bed nuclei of the stria terminalis BST Cart-Tg1-Cre 176886238 -2.80 0.25 4.90 0 Bed nuclei of the stria terminalis BST Crh-IRES-Cre (ZJH) 204832917 0.38 0.50 3.90 0 Bed nuclei of the stria terminalis BST Erbb4-2ACreERT2 167026321 0.02 0.50 3.58 0 Bed nuclei of the stria terminalis BST Erbb4-2ACreERT2 194948535 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 294005186 0.38 0.70 5.00 0 Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 302016815 0.50 0.90 4.85 0 Bed nuclei of the stria terminalis BST Gad2-IRES-Cre 303537993 0.50 0.50 3.90 0 Bed nuclei of the stria terminalis BST Gpr26Cre_KO250 305026146 0.26 0.35 4.60 0 Bed nuclei of the stria terminalis BST Htr2aCre_KM207 301947600 0.14 1.00 4.07 0 Bed nuclei of the stria terminalis BST Htr3aCre_NO152 305645843 0.02 0.50 3.58 0 Bed nuclei of the stria terminalis BST Ppp1r17Cre_NL146 267763584 -0.10 2.55 4.00 30 Bed nuclei of the stria terminalis BST Ppp1r17Cre_NL146 267764292 0.38 0.50 3.90 0 Bed nuclei of the stria terminalis BST Rbp4-Cre_KL100 308386222 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Sim1-Cre 159095796 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Sim1-Cre 159375036 0.02 0.50 3.58 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 12 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Bed nuclei of the stria terminalis BST Sim1-Cre 181786681 0.38 0.02 4.20 0 Bed nuclei of the stria terminalis BST Sim1-Cre 241279971 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Slc17a6-IRESCre 167654731 0.10 0.40 3.67 0 Bed nuclei of the stria terminalis BST Slc6a3-Cre 175739085 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Sst-IRES-Cre 304760810 -0.22 2.75 4.03 30 Bed nuclei of the stria terminalis BST Tac2-IRES2-Cre 265138021 0.14 1.00 4.07 0 Bed nuclei of the stria terminalis, posterior division BSTpr Htr2aCre_KM207 300236763 0.02 0.50 3.58 0 Bed nucleus of the accessory olfactory tract BA Slc17a6-IRESCre 303578324 -1.06 1.70 5.55 0 Bed nucleus of the anterior commissure BAC Cck-IRES-Cre 159433187 0.10 0.40 3.67 0 Caudoputamen CP C57BL/6J 100142580 0.14 1.75 2.53 0 Caudoputamen CP C57BL/6J 112307754 -0.70 2.70 2.39 0 Caudoputamen CP C57BL/6J 112458831 0.14 1.75 2.53 0 Caudoputamen CP C57BL/6J 113505468 0.62 0.29 5.14 -30 Caudoputamen CP C57BL/6J 113766038 -0.70 2.17 1.92 0 Caudoputamen CP C57BL/6J 114399934 0.98 2.65 3.19 0 Caudoputamen CP C57BL/6J 120570964 -1.34 3.00 2.82 0 Caudoputamen CP C57BL/6J 124059700 0.98 0.95 2.12 0 Caudoputamen CP C57BL/6J 127711803 0.62 0.29 5.14 -30 Caudoputamen CP C57BL/6J 127762867 -0.70 2.17 1.92 0 Caudoputamen CP C57BL/6J 146553266 0.98 0.95 2.12 0 Caudoputamen CP C57BL/6J 148198052 0.98 1.90 2.10 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 13 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Caudoputamen CP C57BL/6J 158916311 0.98 1.90 2.10 0 Caudoputamen CP C57BL/6J 175072215 -0.22 3.25 2.90 0 Caudoputamen CP C57BL/6J 180982124 -0.22 3.25 2.90 0 Caudoputamen CP C57BL/6J 272824561 1.42 2.25 2.85 0 Caudoputamen CP Chat-IRES-Cre 183009881 -1.22 3.05 2.37 0 Caudoputamen CP Chat-IRES-Cre 292959343 0.98 0.95 2.12 0 Caudoputamen CP Cux2-CreERT2 292620968 0.98 2.65 3.19 0 Caudoputamen CP Drd1a-Cre 159223001 0.98 0.95 2.12 0 Caudoputamen CP Drd1a-Cre 159941339 -0.70 2.70 2.39 0 Caudoputamen CP Drd1a-Cre 159942097 -0.70 2.70 3.40 0 Caudoputamen CP Drd1a-Cre 160537018 0.98 1.90 1.95 0 Caudoputamen CP Drd1a-Cre 160537796 0.98 1.05 3.12 0 Caudoputamen CP Drd2-Cre_ER44 127140981 0.14 1.75 2.53 0 Caudoputamen CP Drd2-Cre_ER44 127224133 0.98 0.95 2.12 0 Caudoputamen CP Drd2-Cre_ER44 155736539 -0.70 2.70 3.40 0 Caudoputamen CP Drd2-Cre_ER44 155737254 0.98 0.95 2.12 0 Caudoputamen CP Drd2-Cre_ER44 156670520 -0.70 2.70 2.39 0 Caudoputamen CP Drd2-Cre_ER44 158019342 0.96 1.90 1.95 0 Caudoputamen CP Drd2-Cre_ER44 159329308 0.98 1.05 3.12 0 Caudoputamen CP Drd2-Cre_ER44 160540013 -1.34 2.80 1.84 0 Caudoputamen CP Drd2-Cre_ER44 175732996 -1.34 2.80 1.84 0 Caudoputamen CP Gabrr3Cre_KC112 161176690 0.38 2.80 2.76 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 14 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Caudoputamen CP Gad2-IRES-Cre 157911832 -0.70 2.70 2.39 0 Caudoputamen CP Ntrk1-IRES-Cre 265929968 -1.22 3.05 2.37 0 Caudoputamen CP Ntrk1-IRES-Cre 287994474 -1.34 2.80 1.84 0 Caudoputamen CP Ntrk1-IRES-Cre 287995180 -0.70 2.70 2.39 0 Caudoputamen CP Ntrk1-IRES-Cre 310175667 0.98 0.95 2.12 0 Caudoputamen CP Pcdh9-Cre 286311648 -1.34 2.80 1.84 0 Caudoputamen CP Penk-2ACreERT2 278434443 0.14 1.75 2.53 0 Caudoputamen CP Plxnd1-Cre 293366035 -1.34 2.80 1.84 0 Caudoputamen CP Plxnd1-Cre 293366741 -0.70 2.17 1.92 0 Caudoputamen CP Ppp1r17Cre_NL146 286649703 -2.18 3.25 3.60 0 Caudoputamen CP Slc32a1-IRESCre 264095536 -2.92 1.75 3.45 0 Caudoputamen CP Th-Cre_FI172 272697238 -1.22 3.05 2.37 0 Central amygdalar nucleus CEA C57BL/6J 112459547 -1.22 2.77 3.80 0 Central amygdalar nucleus CEA C57BL/6J 117317884 -1.46 3.55 3.70 0 Central amygdalar nucleus CEA C57BL/6J 120282354 -1.46 3.55 3.70 0 Central amygdalar nucleus CEA C57BL/6J 146795148 -0.58 1.75 4.50 0 Central amygdalar nucleus CEA C57BL/6J 175072921 -0.70 2.20 5.00 0 Central amygdalar nucleus CEA Crh-IRES-Cre (ZJH) 267152406 -0.94 2.25 4.47 0 Central amygdalar nucleus CEA Erbb4-2ACreERT2 120281646 -0.94 2.43 4.47 0 Central amygdalar nucleus CEA Erbb4-2ACreERT2 120435569 -1.22 2.77 3.80 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 15 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Central amygdalar nucleus CEA Etv1-CreERT2 181889764 -1.06 2.70 3.90 0 Central amygdalar nucleus CEA Etv1-CreERT2 181890477 -1.22 2.34 4.75 0 Central amygdalar nucleus CEA Etv1-CreERT2 286774064 -1.06 2.70 3.90 0 Central amygdalar nucleus CEA Prkcd-GluClaCFP-IRES-Cre 265945645 -1.82 2.65 4.25 0 Central amygdalar nucleus CEA Slc18a2Cre_OZ14 265648940 -0.94 2.25 4.47 0 Central amygdalar nucleus CEA Tac2-IRES2-Cre 241279261 -0.94 2.25 4.47 0 Central amygdalar nucleus, capsular part CEAc C57BL/6J 127761449 -1.06 2.50 4.84 0 Central lateral nucleus of the thalamus CL Crh-IRES-Cre (BL) 182805965 -0.58 1.00 2.93 0 Central lateral nucleus of the thalamus CL Gal-Cre_KI87 175817683 -1.58 0.68 2.73 0 Central lateral nucleus of the thalamus CL Grm2-Cre_MR90 175740500 -1.58 0.68 2.73 0 Central lateral nucleus of the thalamus CL Rbp4-Cre_KL100 183174303 -2.06 1.25 2.97 0 Central linear nucleus raphe CLI Calb2-IRES-Cre 301765327 -4.16 0.25 5.65 0 Central linear nucleus raphe CLI Syt17-Cre_NO14 127651139 -3.28 0.36 4.13 0 Central medial nucleus of the thalamus CM C57BL/6J 147135107 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM C57BL/6J 147787606 -1.34 0.32 4.05 0 Central medial nucleus of the thalamus CM C57BL/6J 158841171 -1.46 0.13 4.00 0 Central medial nucleus of the thalamus CM C57BL/6J 273025166 -1.22 0.13 4.00 0 Central medial nucleus of the thalamus CM Calb2-IRES-Cre 182888003 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM Gal-Cre_KI87 168004394 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM Grm2-Cre_MR90 284665639 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM Grp-Cre_KH288 183057424 -1.06 0.20 3.40 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 16 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Central medial nucleus of the thalamus CM Grp-Cre_KH288 301324895 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM Lypd6Cre_KL156 298050269 -1.06 0.20 3.40 0 Central medial nucleus of the thalamus CM Lypd6Cre_KL156 303710632 -1.46 0.13 1.45 0 Central medial nucleus of the thalamus CM Plxnd1-Cre 293367448 -1.34 0.50 3.40 0 Central medial nucleus of the thalamus CM Plxnd1-Cre 301538025 -1.06 0.20 3.40 0 Claustrum CLA A930038C07RikTg1-Cre 292375491 1.10 3.25, 3.00 1.90, 2.35 0 Claustrum CLA C57BL/6J 180436360 -0.34 4.00 2.60 0 Claustrum CLA Cux2-IRES-Cre 293473098 -0.34 3.85 3.00 0 Claustrum CLA Cux2-IRES-Cre 296047806 1.78 2.40, 2.80 2.24 0 Claustrum CLA Oxtr-Cre_ON66 278171908 1.70 1.85 2.83 0 Claustrum CLA Oxtr-Cre_ON66 292372636 -1.46 3.75 3.40 0 Copula pyramidis COPY Prkcd-GluClaCFP-IRES-Cre 267611175 -6.12 2.25 2.90 0 Cortical amygdalar area, posterior part, lateral zone COApl C57BL/6J 115958115 -1.22 2.34 4.75 0 Cortical amygdalar area, posterior part, lateral zone COApl C57BL/6J 122641078 -0.58 2.75 5.40 0 Cortical amygdalar area, posterior part, lateral zone COApl C57BL/6J 129573239 -1.70 2.75 5.25 0 Cortical amygdalar area, posterior part, lateral zone COApl C57BL/6J 277480964 -2.30 2.75 4.70 0 Cortical amygdalar area, posterior part, lateral zone COApl Gad2-IRES-Cre 305124396 -0.46 2.20 5.22 0 Cortical amygdalar area, posterior part, lateral zone COApl Grik4-Cre 168302154 -1.70 2.75 5.25 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 17 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Cortical amygdalar area, posterior part, lateral zone COApl Rbp4-Cre_KL100 304721447 -1.34 1.75 4.50 0 Cortical amygdalar area, posterior part, lateral zone COApl Slc17a6-IRESCre 266962653 -1.70 2.75 5.25 0 Cortical amygdalar area, posterior part, lateral zone COApl Slc17a7-IRES2Cre 267150949 -1.70 2.75 5.25 0 Cortical amygdalar area, posterior part, medial zone COApm C57BL/6J 114249084 -2.70 2.80 5.07 0 Cortical amygdalar area, posterior part, medial zone COApm C57BL/6J 125802444 -2.46 2.75 4.75 0 Cortical amygdalar area, posterior part, medial zone COApm Sim1-Cre 170946889 -1.58 1.80 5.45 0 Cortical amygdalar area, posterior part, medial zone COApm Slc32a1-IRESCre 299623085 -2.46 2.75 4.75 0 Crus 1 ANcr1 C57BL/6J 112827872 -6.48 3.00 0.98 0 Crus 1 ANcr1 Gabra6-IRESCre 181116850 -6.48 2.50 0.57 0 Crus 1 ANcr1 Grm2-Cre_MR90 287879384 -6.48 2.50 0.57 0 Crus 1 ANcr1 Grm2-Cre_MR90 301324157 -6.48 2.50 0.57 0 Crus 1 ANcr1 Pcp2Cre_GN135 147633169 -6.48 2.50 0.57 0 Crus 1 ANcr1 Pvalb-IRES-Cre 167201465 -6.48 2.50 0.57 0 Crus 2 ANcr2 C57BL/6J 142654808 -6.48 2.50 0.57 0 Crus 2 ANcr2 Pcp2Cre_GN135 168230532 -6.48 3.00 0.98 0 Cuneiform nucleus CUN C57BL/6J 120571672 -5.02 1.20 2.30 0 Cuneiform nucleus CUN C57BL/6J 126522350 -4.48 1.15 2.80 0 Dentate gyrus DG A930038C07RikTg1-Cre 298232793 1.70 0.40 2.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 18 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dentate gyrus DG Adcyap1-2A-Cre 287247261 -3.52 2.50 3.50 0 Dentate gyrus DG C57BL/6J 100141214 -1.70 0.70 2.04 0 Dentate gyrus DG C57BL/6J 100148143 -1.70 0.70 2.04 0 Dentate gyrus DG C57BL/6J 112167395 interaural 0.00 1.50 1.77 0 Dentate gyrus DG C57BL/6J 112672268 -4.04 3.25 2.60 0 Dentate gyrus DG C57BL/6J 112745787 -2.30 1.75 1.66 0 Dentate gyrus DG C57BL/6J 113166056 -3.52 2.50 3.50 0 Dentate gyrus DG C57BL/6J 114008220 -2.92 1.85 1.95 0 Dentate gyrus DG C57BL/6J 114430043 -3.52 2.75 2.34 0 Dentate gyrus DG C57BL/6J 272970039 -0.80 0.25 2.45 0 Dentate gyrus DG Drd3-Cre_KI198 301122593 -1.70 0.70 2.04 0 Dentate gyrus DG Gad2-IRES-Cre 305400137 -1.70 0.70 2.04 0 Dentate gyrus DG Gal-Cre_KI87 266173339 -3.52 2.75 2.34 0 Dentate gyrus DG Grik4-Cre 113933871 -2.30 1.75 1.66 0 Dentate gyrus DG Grik4-Cre 114009636 -1.70 0.70 2.04 0 Dentate gyrus DG Grik4-Cre 114047146 -2.92 1.85 1.95 0 Dentate gyrus DG Grik4-Cre 182029174 -3.52 2.50 3.50 0 Dentate gyrus DG Grm2-Cre_MR90 264709761 -2.30 1.75 1.66 0 Dentate gyrus DG Grm2-Cre_MR90 264872385 -3.52 2.75 2.34 0 Dentate gyrus DG Grm2-Cre_MR90 287097454 -1.70 0.70 2.04 0 Dentate gyrus DG Grm2-Cre_MR90 287171983 -2.92 1.85 1.95 0 Dentate gyrus DG Lypd6Cre_KL156 299857813 -1.70 0.70 2.04 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 19 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dentate gyrus DG Nos1-CreERT2 301327022 -1.70 0.70 2.04 0 Dentate gyrus DG Oxtr-Cre_ON66 301422682 -1.70 0.70 2.04 0 Dentate gyrus DG Pomc-Cre (BL) 159996191 -1.70 0.70 2.04 0 Dentate gyrus DG Pomc-Cre (BL) 160079360 -3.52 2.75 2.34 0 Dentate gyrus DG Pomc-Cre (ST) 113780276 -2.30 1.75 1.66 0 Dentate gyrus DG Ppp1r17Cre_NL146 278504263 -1.34 0.75 2.24 0 Dentate gyrus DG Ppp1r17Cre_NL146 308550233 -1.70 0.70 2.04 0 Dentate gyrus DG Rbp4-Cre_KL100 182295393 -1.70 0.70 2.04 0 Dentate gyrus DG Rbp4-Cre_KL100 183376982 -2.92 1.85 1.95 0 Dentate gyrus DG Rbp4-Cre_KL100 266250904 -2.30 1.75 1.66 0 Dentate gyrus DG Rbp4-Cre_KL100 266409949 -3.52 2.75 2.34 0 Dentate gyrus DG Slc17a7-IRES2Cre 293788700 -3.16 2.10 2.85 0 Dentate gyrus DG Slc17a7-IRES2Cre 293787994 -2.18 1.45 2.44 0 Dentate gyrus DG Slc32a1-IRESCre 305320171 -1.70 0.70 2.04 0 Dentate gyrus DG Syt17-Cre_NO14 288322797 -1.70 0.70 2.04 0 Dentate gyrus DG Syt17-Cre_NO14 293011049 -2.30 1.75 1.66 0 Dentate gyrus DG Syt17-Cre_NO14 293011759 -3.52 2.75 2.34 0 Dentate gyrus DG Syt17-Cre_NO14 293115527 -1.34 0.75 2.24 0 Dentate nucleus DN C57BL/6J 268389532 -6.24 2.20 2.25 0 Dentate nucleus DN Gad2-IRES-Cre 304675254 -6.12 2.25 2.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 20 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dentate nucleus DN Slc17a6-IRESCre 286608092 -5.88 2.25 2.19 0 Diagonal band nucleus NDB Chat-IRES-Cre 167200755 0.50 0.81 4.84 0 Diagonal band nucleus NDB Chat-IRES-Cre 177605425 0.98 0.25 4.60 0 Diagonal band nucleus NDB Ntrk1-IRES-Cre 286319739 0.62 1.20 4.85 0 Dorsal auditory area AUDd C57BL/6J 115958825 -3.08 4.00 0.80 0 Dorsal auditory area AUDd C57BL/6J 139519496 -2.46 4.25 0.81 0 Dorsal auditory area AUDd C57BL/6J 146858006 -3.08 4.00 0.80 0 Dorsal auditory area AUDd C57BL/6J 158314278 -2.46 4.00 0.65 0 Dorsal auditory area AUDd C57BL/6J 180073473 -3.40 4.00 1.07 0 Dorsal auditory area AUDd Cux2-IRES-Cre 176430283 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Erbb4-2ACreERT2 156743264 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Nr5a1-Cre 114752488 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Ntsr1Cre_GN220 120494024 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Pvalb-IRES-Cre 160080068 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Tac1-IRES2-Cre 181372049 -2.46 4.25 0.81 0 Dorsal auditory area AUDd Tac2-IRES2-Cre 268075711 -2.46 4.35 0.90 0 Dorsal cochlear nucleus DCO C57BL/6J 143515102 -5.52 1.16 3.70 -20 Dorsal cochlear nucleus DCO C57BL/6J 146794439 -5.20 1.95 3.50 0 Dorsal cochlear nucleus DCO Crh-IRES-Cre (BL) 167213641 -6.12 2.25 2.80 0 Dorsal cochlear nucleus DCO Crh-IRES-Cre (BL) 266839784 -6.12 2.25 2.90 0 Dorsal cochlear nucleus DCO Gad2-IRES-Cre 287664997 -6.12 2.25 2.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 21 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dorsal cochlear nucleus DCO Pnmt-Cre 177903648 -6.12 2.25 2.80 0 Dorsal cochlear nucleus DCO Prkcd-GluClaCFP-IRES-Cre 292319155 -6.12 2.25 2.90 0 Dorsal cochlear nucleus DCO Slc17a6-IRESCre 286556914 -6.12 2.25 2.90 0 Dorsal cochlear nucleus DCO Slc6a5Cre_KF109 160152987 -6.12 2.25 2.80 0 Dorsal motor nucleus of the vagus nerve DMX Chat-IRES-Cre 264564375 0.00 calamus (-7.32 bregma) 0.25 0.48 0 Dorsal motor nucleus of the vagus nerve DMX Gad2-IRES-Cre 303536573 0 calamus 0.25 0.48 0 Dorsal motor nucleus of the vagus nerve DMX Nxph4-2ACreERT2 304612686 0 calamus 0.05 0.20 0 Dorsal motor nucleus of the vagus nerve DMX Ppp1r17Cre_NL146 268323342 0.00 calamus (-7.32 bregma) 0.25 0.48 0 Dorsal motor nucleus of the vagus nerve DMX Slc18a2Cre_OZ14 287096578 0.00 calamus (-7.32 bregma) 0.25 0.48 0 Dorsal motor nucleus of the vagus nerve DMX Slc6a3-Cre 171021122 0.00 calamus (-7.32 bregma) 0.25 0.48 0 Dorsal motor nucleus of the vagus nerve DMX Syt17-Cre_NO14 263784128 0.00 calamus (-7.32 bregma) 0.25 0.48 0 Dorsal nucleus raphe DR C57BL/6J 114155923 -4.24 0.52 2.86 10 Dorsal nucleus raphe DR Drd3-Cre_KI196 300111793 -3.80 0.04 2.85 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 22 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dorsal nucleus raphe DR Slc6a4Cre_ET33 128055110 -4.24 0.52 2.86 10 Dorsal nucleus raphe DR Slc6a4Cre_ET33 129564675 -4.36 0.18 2.10 0 Dorsal nucleus raphe DR Slc6a4Cre_ET33 168300027 -3.88 0.20 3.30 0 Dorsal nucleus raphe DR Slc6a4CreERT2_EZ13 114155190 -4.24 0.52 2.86 10 Dorsal nucleus raphe DR Slc6a4CreERT2_EZ13 114248377 -4.36 0.18 2.10 0 Dorsal nucleus raphe DR Th-Cre_FI172 266500714 -4.24 0.52 2.86 10 Dorsal part of the lateral geniculate complex LGd C57BL/6J 100141598 -2.30 2.00 2.44 0 Dorsal part of the lateral geniculate complex LGd Gal-Cre_KI87 266248776 -2.30 2.00 2.60 0 Dorsal part of the lateral geniculate complex LGd Htr2aCre_KM207 298004028 -2.00 2.15 2.60 0 Dorsal part of the lateral geniculate complex LGd Htr2aCre_KM207 298003295 -2.30 2.00 2.60 0 Dorsal part of the lateral geniculate complex LGd Prkcd-GluClaCFP-IRES-Cre 292320572 -2.00 2.15 2.60 0 Dorsal part of the lateral geniculate complex LGd Scnn1a-Tg2-Cre 156198187 -2.30 2.00 2.44 0 Dorsal part of the lateral geniculate complex LGd Scnn1a-Tg2-Cre 263241470 -2.30 2.00 2.60 0 Dorsal part of the lateral geniculate complex LGd Slc17a6-IRESCre 293914056 -2.30 2.00 2.60 0 Dorsal part of the lateral geniculate complex LGd Slc17a6-IRESCre 293914766 -2.00 2.15 2.60 0 Dorsal part of the lateral geniculate complex LGd Slc17a7-IRES2Cre 293787288 -2.30 2.00 2.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 23 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dorsal part of the lateral geniculate complex LGd Slc18a2Cre_OZ14 287458189 -2.00 2.15 2.60 0 Dorsal part of the lateral geniculate complex LGd Slc18a2Cre_OZ14 287458895 -2.30 2.00 2.60 0 Dorsal part of the lateral geniculate complex LGd Slc18a2Cre_OZ14 301735795 -2.30 2.00 2.60 0 Dorsal peduncular area DP C57BL/6J 112597496 1.70 0.25 2.47 0 Dorsal premammillary nucleus PMd C57BL/6J 146659588 -1.46 0.39 5.50 0 Dorsal premammillary nucleus PMd Tac1-IRES2-Cre 294316542 -2.70 0.13 5.20 0 Dorsomedial nucleus of the hypothalamus DMH C57BL/6J 175106053 -0.58 0.20 4.75 0 Dorsomedial nucleus of the hypothalamus DMH Cart-Tg1-Cre 298833739 -1.46 0.39 5.50 0 Dorsomedial nucleus of the hypothalamus DMH Gad2-IRES-Cre 287538943 -1.50 0.35 5.30 0 Dorsomedial nucleus of the hypothalamus DMH Gal-Cre_KI87 178283239 -1.50 0.35 5.20 0 Dorsomedial nucleus of the hypothalamus DMH Gal-Cre_KI87 266248065 -1.50 0.35 5.20 0 Dorsomedial nucleus of the hypothalamus DMH Hdc-Cre_IM1 168616827 -1.70 0.35 4.90 0 Dorsomedial nucleus of the hypothalamus DMH Ins2-Cre 265813096 -1.22 0.94 5.04 10 Dorsomedial nucleus of the hypothalamus DMH Lepr-IRES-Cre 113314337 -1.46 0.39 5.30 0 Dorsomedial nucleus of the hypothalamus DMH Lepr-IRES-Cre 160317628 -1.70 0.36 4.89 0 Dorsomedial nucleus of the hypothalamus DMH Nr5a1-Cre 182336846 -1.46 0.39 5.30 0 Dorsomedial nucleus of the hypothalamus DMH Ppp1r17Cre_NL146 308641549 -1.50 0.35 5.30 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 24 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Dorsomedial nucleus of the hypothalamus DMH Rasgrf2-2A-dCre 313325371 -1.46 0.39 5.50 0 Dorsomedial nucleus of the hypothalamus DMH Sim1-Cre 159222295 -0.94 0.25 4.52 0 Dorsomedial nucleus of the hypothalamus DMH Sim1-Cre_KJ18 266837456 -1.46 0.39 5.50 0 Ectorhinal area ECT A930038C07RikTg1-Cre 264630726 -4.36 4.25 1.40 0 Ectorhinal area ECT A930038C07RikTg1-Cre 286837316 -4.04 3.80 1.90 0 Ectorhinal area ECT C57BL/6J 180403712 -2.00 4.20 2.15 0 Ectorhinal area ECT C57BL/6J 272414403 -4.36 4.25 1.40 0 Ectorhinal area ECT Cux2-IRES-Cre 278317239 -4.04 3.80 1.90 0 Ectorhinal area ECT Gpr26Cre_KO250 301264977 -4.36 4.00 1.25 0 Ectorhinal area ECT Gpr26Cre_KO250 301265683 -4.36 4.25 1.35 0 Ectorhinal area ECT Rbp4-Cre_KL100 182794184 -4.36 4.25 1.40 0 Endopiriform nucleus, dorsal part EPd C57BL/6J 158321996 -0.22 3.70 3.25 0 Endopiriform nucleus, dorsal part EPd Gad2-IRES-Cre 305403845 -1.46 4.00 3.70 0 Endopiriform nucleus, dorsal part EPd Htr2aCre_KM207 308549214 -1.46 3.75 3.40 0 Endopiriform nucleus, dorsal part EPd Kcnc2-Cre 126853068 0.98 2.85 3.14 0 Endopiriform nucleus, dorsal part EPd Kcnc2-Cre 126863090 -1.46 3.75 3.40 0 Endopiriform nucleus, dorsal part EPd Oxtr-Cre_ON66 267762146 0.98 2.65 3.19 0 Endopiriform nucleus, dorsal part EPd Oxtr-Cre_ON66 267762859 0.98 2.85 3.14 0 Endopiriform nucleus, dorsal part EPd Syt17-Cre_NO14 187268452 0.98 3.00 3.14 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 25 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Endopiriform nucleus, ventral part EPv Efr3aCre_NO108 299244730 -0.94 2.60 4.60 0 Entorhinal area ENT Grm2-Cre_MR90 267747690 -4.21 3.40 2.20, 2.60 0 Entorhinal area ENT Scnn1a-Tg2-Cre 268041795 -4.59 3.40 2.20, 2.60 0 Entorhinal area ENT Scnn1a-Tg3-Cre 287770700 -4.43 3.40 2.20, 2.60 0 Entorhinal area ENT Sst-IRES-Cre 288321385 -4.72 3.40 2.20, 2.60 0 Entorhinal area ENT Syt17-Cre_NO14 288322091 -4.16 3.80 3.00 0 Entorhinal area, lateral part ENTl A930038C07RikTg1-Cre 298798846 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl A930038C07RikTg1-Cre 298797996 -4.16 3.80 3.00 0 Entorhinal area, lateral part ENTl C57BL/6J 114472145 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl C57BL/6J 126116848 -3.40 4.10 3.05 0 Entorhinal area, lateral part ENTl C57BL/6J 127397469 -2.70 4.25 2.75 0 Entorhinal area, lateral part ENTl C57BL/6J 142654100 -4.36 4.00 1.25 0 Entorhinal area, lateral part ENTl C57BL/6J 146553971 1.18 0.70 4.15 0 Entorhinal area, lateral part ENTl C57BL/6J 180297139 -4.36 3.90 1.40 0 Entorhinal area, lateral part ENTl Chrna2Cre_OE25 299857096 -4.16 3.80 3.00 0 Entorhinal area, lateral part ENTl Cux2-CreERT2 181859467 -4.72 3.37 2.11, 2.60 0 Entorhinal area, lateral part ENTl Cux2-IRES-Cre 263974698 -4.36 4.25 1.40 0 Entorhinal area, lateral part ENTl Cux2-IRES-Cre 272779830 -4.36 4.25 1.30 0 Entorhinal area, lateral part ENTl Cux2-IRES-Cre 287953223 -4.22 3.40 2.20 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 26 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Entorhinal area, lateral part ENTl Cux2-IRES-Cre 287952517 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Drd3-Cre_KI196 293702482 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Grm2-Cre_MR90 183225124 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Htr2aCre_KM207 301988879 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Ntsr1Cre_GN220 159602279 -4.24 4.00 1.65 0 Entorhinal area, lateral part ENTl Otof-Cre 167212932 -3.40 4.10 3.05 0 Entorhinal area, lateral part ENTl Otof-Cre 181891184 -4.16 3.80 3.00 0 Entorhinal area, lateral part ENTl Otof-Cre 182226133 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Pcdh9-Cre 267211671 -4.60 3.75 1.55 0 Entorhinal area, lateral part ENTl Penk-IRES2-Cre 305973112 -4.16 3.80 3.00 0 Entorhinal area, lateral part ENTl Plxnd1-Cre 301464114 -2.70 2.80 5.07 0 Entorhinal area, lateral part ENTl Rbp4-Cre_KL100 232311959 -4.24 4.00 1.65 0 Entorhinal area, lateral part ENTl Rbp4-Cre_KL100 286483411 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Scnn1a-Tg3-Cre 287769992 -4.04 3.80 1.90 0 Entorhinal area, lateral part ENTl Syt17-Cre_NO14 293009265 -3.16 4.25 2.76 0 Entorhinal area, lateral part ENTl Wfs1-Tg2CreERT2 278435864 -4.32 3.40 2.20, 2.60 0 Entorhinal area, lateral part ENTl Wfs1-Tg2CreERT2 278435152 -4.35 3.40 2.20, 2.60 0 Entorhinal area, lateral part ENTl Wfs1-Tg3CreERT2 182516286 -3.16 4.25 2.76 0 Entorhinal area, medial part, dorsal zone ENTm C57BL/6J 112672974 -4.72 3.37 2.11, 2.60 0 Entorhinal area, medial part, dorsal zone ENTm C57BL/6J 113226232 -4.16 3.80 3.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 27 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Entorhinal area, medial part, dorsal zone ENTm C57BL/6J 127139568 -4.48 3.00 3.44 0 Entorhinal area, medial part, dorsal zone ENTm Calb1-2A-dgCre 293750063 -4.72 3.40 2.20, 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Cux2-CreERT2 194947823 -4.96 3.10 2.65 0 Entorhinal area, medial part, dorsal zone ENTm Cux2-CreERT2 264873092 -4.45 3.40 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Cux2-CreERT2 264873809 -4.58 3.40 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Drd3-Cre_KI196 300078194 -4.72 3.40 2.2, 2.6 0 Entorhinal area, medial part, dorsal zone ENTm Grik4-Cre 267998328 -4.04 3.40 2.20, 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Grik4-Cre 267999034 -4.23 3.40 2.20, 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Htr2aCre_KM207 300319630 -4.16 3.80 3.00 0 Entorhinal area, medial part, dorsal zone ENTm Nos1-CreERT2 299403823 -4.40 3.40 2.2, 2.6 0 Entorhinal area, medial part, dorsal zone ENTm Pcdh9-Cre 308642254 -4.72 3.40 2.20 0 Entorhinal area, medial part, dorsal zone ENTm Pcdh9Cre_NP276 308721177 -4.60 2.40 2.95 0 Entorhinal area, medial part, dorsal zone ENTm Scnn1a-Tg2-Cre 299447153 -4.34 3.40 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Scnn1a-Tg2-Cre 302014692 -4.47 3.40 2.65 0 Entorhinal area, medial part, dorsal zone ENTm Syt17-Cre_NO14 286484879 -4.72 3.40 2.20, 2.60 0 Entorhinal area, medial part, dorsal zone ENTm Wfs1-Tg3CreERT2 167793416 -4.16 3.80 3.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 28 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Facial motor nucleus VII C57BL/6J 123663689 -5.34 1.11 4.80 0 Facial motor nucleus VII C57BL/6J 147214398 -5.02 1.11 4.80 0 Facial motor nucleus VII Chat-IRES-Cre 157712456 -6.00 1.15 4.57 0 Facial motor nucleus VII Chat-IRES-Cre 301800314 -4.16 1.00 5.70 0 Facial motor nucleus VII Grik4-Cre 113766744 -6.00 1.15 4.57 0 Facial motor nucleus VII Scnn1a-Tg2-Cre 177905562 -6.00 1.15 4.57 0 Fastigial nucleus FN C57BL/6J 127650431 -6.36 0.75 2.40 0 Field CA1 CA1 C57BL/6J 100147861 -1.70 1.60 1.17 0 Field CA1 CA1 C57BL/6J 100148443 -3.52 3.50 2.07 0 Field CA1 CA1 C57BL/6J 116900714 -2.30 1.25 1.25 0 Field CA1 CA1 C57BL/6J 120436274 -2.30 1.25 1.25 0 Field CA1 CA1 C57BL/6J 120494729 -2.46 2.50 1.34 0 Field CA1 CA1 Chrna2Cre_OE25 297894255 -4.04 3.80 1.90 0 Field CA1 CA1 Cux2-IRES-Cre 294397907 -4.04 3.80 1.90 0 Field CA1 CA1 Drd3-Cre_KI198 301119459 -2.46 2.50 1.34 0 Field CA1 CA1 Drd3-Cre_KI198 301130077 -1.70 1.60 1.17 0 Field CA1 CA1 Etv1-CreERT2 171019004 -1.70 1.60 1.17 0 Field CA1 CA1 Etv1-CreERT2 175718634 -2.92 3.00 3.45 0 Field CA1 CA1 Etv1-CreERT2 181093729 -3.52 3.50 2.07 0 Field CA1 CA1 Gad2-IRES-Cre 305380411 -2.46 2.50 1.34 0 Field CA1 CA1 Gpr26Cre_KO250 286554017 -2.46 2.50 1.34 0 Field CA1 CA1 Kcnc2-Cre 182843806 -2.46 2.50 1.34 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 29 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Field CA1 CA1 Nos1-CreERT2 301325601 -2.46 2.50 1.34 0 Field CA1 CA1 Ppp1r17Cre_NL146 278503555 -1.70 0.70 2.04 0 Field CA1 CA1 Ppp1r17Cre_NL146 292479421 -1.70 0.50 1.70 0 Field CA1 CA1 Ppp1r17Cre_NL146 292532771 -2.92 1.17 1.40 0 Field CA1 CA1 Ppp1r17Cre_NL146 292532065 -3.52 2.50 1.35 0 Field CA1 CA1 Sim1-Cre 181777177 -1.70 0.50 1.70 0 Field CA1 CA1 Slc17a7-IRES2Cre 267104205 -2.46 2.50 1.34 0 Field CA1 CA1 Slc17a7-IRES2Cre 286317619 -1.70 0.70 2.04 0 Field CA1 CA1 Slc32a1-IRESCre 305381127 -2.46 2.50 1.34 0 Field CA1 CA1 Syt17-Cre_NO14 286610923 -3.52 3.50 2.07 0 Field CA1 CA1 Vipr2-Cre_KE2 180405830 -2.46 2.50 1.34 0 Field CA1 CA1 Vipr2-Cre_KE2 180520968 -2.30 1.25 1.25 0 Field CA1 CA1 Vipr2-Cre_KE2 182226839 -3.52 3.50 2.07 0 Field CA3 CA3 C57BL/6J 112308468 -2.46 2.60 2.36 0 Field CA3 CA3 C57BL/6J 112745073 -1.70 2.00 1.85 0 Field CA3 CA3 C57BL/6J 113935285 -2.80 2.85 3.00 0 Field CA3 CA3 C57BL/6J 114429338 -2.30 2.97 1.80 0 Field CA3 CA3 C57BL/6J 127649005 -2.92 3.00 3.45 0 Field CA3 CA3 C57BL/6J 180523704 -1.82 2.05 2.42 0 Field CA3 CA3 C57BL/6J 272404772 -2.30 2.75 1.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 30 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Field CA3 CA3 Drd3-Cre_KI198 301120618 -2.46 2.60 2.25 0 Field CA3 CA3 Gad2-IRES-Cre 266488504 -2.54 4.25 3.32 25 Field CA3 CA3 Grik4-Cre 177606858 -2.46 2.60 2.36 0 Field CA3 CA3 Grik4-Cre 177780284 -1.70 2.00 1.85 0 Field CA3 CA3 Grik4-Cre 178382220 -2.80 2.85 3.00 0 Field CA3 CA3 Grik4-Cre 179643824 -2.30 2.97 1.80 0 Field CA3 CA3 Grp-Cre_KH288 179644545 -2.46 2.60 2.36 0 Field CA3 CA3 Grp-Cre_KH288 179902073 -1.70 2.00 1.85 0 Field CA3 CA3 Grp-Cre_KH288 182615063 -2.30 2.97 1.80 0 Field CA3 CA3 Grp-Cre_KH288 182615771 -2.80 2.85 3.00 0 Field CA3 CA3 Kcnc2-Cre 182933935 -2.46 2.60 2.36 0 Field CA3 CA3 Nos1-CreERT2 301326316 -2.46 2.60 2.25 0 Field CA3 CA3 Oxtr-Cre_ON66 301421960 -2.46 2.60 2.25 0 Field CA3 CA3 Ppp1r17Cre_NL146 278318653 -2.46 2.60 2.36 0 Field CA3 CA3 Ppp1r17Cre_NL146 278319402 -1.70 2.00 1.85 0 Field CA3 CA3 Ppp1r17Cre_NL146 278398243 -2.30 2.97 1.80 0 Field CA3 CA3 Ppp1r17Cre_NL146 278399657 -3.52 2.50 3.50 0 Field CA3 CA3 Prkcd-GluClaCFP-IRES-Cre 171274191 -1.70 2.00 1.85 0 Field CA3 CA3 Syt17-Cre_NO14 249402769 -3.08 3.00 3.60 0 Flocculus FL C57BL/6J 112789899 -4.24 2.36 3.58 0 Flocculus FL Nos1-CreERT2 304997333 -5.20 1.25 2.80 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 31 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Gigantocellular reticular nucleus GRN A930038C07RikTg1-Cre 299995638 0.0 calamus 0.05 1.00 0 Gigantocellular reticular nucleus GRN C57BL/6J 125437921 -6.12 0.35 4.90 0 Gigantocellular reticular nucleus GRN C57BL/6J 126188607 -6.24 0.85 4.40 0 Gigantocellular reticular nucleus GRN C57BL/6J 126710034 -6.48 1.00 4.82 0 Gigantocellular reticular nucleus GRN C57BL/6J 126843905 -6.72 0.50 4.55 0 Gigantocellular reticular nucleus GRN C57BL/6J 127041832 -0.24 calamus (-7.56 bregma) 0.50 1.75 0 Gigantocellular reticular nucleus GRN C57BL/6J 147706228 -5.02 0.50 5.25 0 Gigantocellular reticular nucleus GRN Dbh-Cre_KH212 287029894 -5.68 0.80 5.20 0 Gigantocellular reticular nucleus GRN Gad2-IRES-Cre 287876212 -6.12 0.35 4.90 0 Gigantocellular reticular nucleus GRN Pdzk1ip1Cre_KD31 182030590 -5.34 1.11 4.80 0 Gigantocellular reticular nucleus GRN Slc17a6-IRESCre 286609510 -6.12 0.35 4.90 0 Gigantocellular reticular nucleus GRN Slc32a1-IRESCre 303468314 -5.88 2.25 5.30 25 Gigantocellular reticular nucleus GRN Slc32a1-IRESCre 305293928 -6.48 1.00 4.90 0 Gigantocellular reticular nucleus GRN Slc6a5Cre_KF109 160081484 -5.88 2.25 5.00 25 Gigantocellular reticular nucleus GRN Slc6a5Cre_KF109 267703239 -5.88 2.25 5.00 25 Globus pallidus, external segment GPe C57BL/6J 158373958 -0.34 1.70 3.58 0 Globus pallidus, external segment GPe Htr2aCre_KM207 300318924 -0.34 1.70 3.58 0 Globus pallidus, external segment GPe Ntrk1-IRES-Cre 265943460 -0.70 1.80 3.95 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 32 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Globus pallidus, external segment GPe Ntrk1-IRES-Cre 265944167 -0.34 1.70 3.58 0 Globus pallidus, internal segment GPi Htr2aCre_KM207 278501857 -0.70 1.80 3.95 0 Globus pallidus, internal segment GPi Ntrk1-IRES-Cre 292960052 -1.34 1.75 4.50 0 Globus pallidus, internal segment GPi Rbp4-Cre_KL100 305024724 -1.70 2.75 5.25 0 Gracile nucleus GR C57BL/6J 114400640 0.00 calamus (-7.20 bregma) 0.25 0.15 0 Gracile nucleus GR Erbb4-2ACreERT2 268321221 0.20 calamus (-7.00 bregma) 0.25 0.15 0 Gracile nucleus GR Sst-IRES-Cre 300843120 0.2 calamus (-7.00 bregma) 0.25 0.15 0 Gustatory areas GU C57BL/6J 180404418 0.38 3.60 2.35 0 Gustatory areas GU C57BL/6J 272737914 1.10 3.25, 3.00 1.90, 2.35 0 Gustatory areas GU Cux2-IRES-Cre 264076854 1.78 2.40, 2.80 2.25 0 Gustatory areas GU Nr5a1-Cre 177892379 1.10 3.25, 3.00 1.90, 2.35 0 Gustatory areas GU Rbp4-Cre_KL100 272928602 1.10 3.25, 3.00 1.90, 2.35 0 Hypoglossal nucleus XII C57BL/6J 127350480 -0.16 calamus (-7.48 bregma) 0.25 0.65 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 33 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Hypoglossal nucleus XII Chat-IRES-Cre 165973664 -0.16 calamus (-7.48 bregma) 0.25 0.65 0 Hypoglossal nucleus XII Chat-IRES-Cre 177606140 -0.16 calamus (-7.48 bregma) 0.35 0.65 0 Hypoglossal nucleus XII Scnn1a-Tg2-Cre 177904363 -0.16 calamus (-7.48 bregma) 0.35 0.65 0 Inferior colliculus IC C57BL/6J 147162027 -4.96 1.40 0.85 0 Inferior colliculus IC Nos1-CreERT2 299761293 -5.02 0.50 0.65 0 Inferior colliculus IC Pdzk1ip1Cre_KD31 183375545 -5.20 1.25 1.30 0 Inferior colliculus IC Pdzk1ip1Cre_KD31 266966337 -5.02 0.50 0.65 0 Inferior colliculus IC Slc17a6-IRESCre 287448038 -5.20 1.25 1.30 0 Inferior colliculus IC Slc17a6-IRESCre 294174290 -4.48 0.50 1.85 0 Inferior colliculus IC Sst-IRES-Cre 305446876 -4.72 1.25 1.10 0 Inferior colliculus, central nucleus ICc C57BL/6J 113368085 -5.20 1.25 1.30 0 Inferior colliculus, central nucleus ICc Slc17a6-IRESCre 287452840 -4.72 1.25 1.10 0 Inferior colliculus, dorsal nucleus ICd C57BL/6J 116905391 -5.02 0.50 0.65 0 Inferior colliculus, external nucleus ICe C57BL/6J 100141596 -4.36 1.59 1.87 0 Inferior colliculus, external nucleus ICe Chrna2Cre_OE25 304857992 -5.20 1.25 1.30 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 34 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Inferior colliculus, external nucleus ICe Nxph4-2ACreERT2 287714197 -4.36 1.59 1.87 0 Inferior colliculus, external nucleus ICe Pvalb-IRES-Cre 277959325 -5.20 1.25 1.30 0 Inferior colliculus, external nucleus ICe Slc17a6-IRESCre 294199114 -4.36 1.87 2.58 0 Inferior colliculus, external nucleus ICe Sst-IRES-Cre 305447664 -5.20 1.25 2.80 0 Inferior olivary complex IO Calb2-IRES-Cre 182890735 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Inferior olivary complex IO Crh-IRES-Cre (BL) 167665302 0.00 calamus (-7.32 bregma) 0.10 2.40 0 Inferior olivary complex IO Crh-IRES-Cre (ZJH) 292622743 -0.24 calamus (-7.56 Bregma) 1.12 2.30 0 Infralimbic area ILA C57BL/6J 157556400 1.70 0.40 2.00 0 Infralimbic area ILA Chrna2Cre_OE25 298272589 1.70 0.40 2.00 0 Infralimbic area ILA Cux2-IRES-Cre 287494320 -4.04 4.00 0.35 30 Infralimbic area ILA Grp-Cre_KH288 266583498 1.70 0.40 2.00 0 Infralimbic area ILA Oxtr-Cre_ON66 294399325 1.70 0.40 2.00 0 Infralimbic area ILA Rbp4-Cre_KL100 286313491 1.70 0.40 2.00 0 Infralimbic area ILA Syt17-Cre_NO14 299653551 1.70 0.40 2.00 0 Infralimbic area ILA Syt6-Cre_KI148 177889243 2.10 0.06, 0.33 1.50 0 Infralimbic area ILA Ucn3-Cre_KF43 266913950 2.68 0.65 1.64 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 35 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Interanterodorsal nucleus of the thalamus IAD Crh-IRES-Cre (BL) 264707643 -5.52 0.88 2.71 0 Intercalated amygdalar nucleus IA C57BL/6J 146012934 -0.94 2.60 4.60 0 Interfascicular nucleus raphe IF C57BL/6J 120572378 -3.52 0.08 4.30 0 Interfascicular nucleus raphe IF Calb2-IRES-Cre 310176384 -3.28 0.36 4.13 0 Interfascicular nucleus raphe IF Erbb4-2ACreERT2 267538735 -3.52 0.08 4.30 0 Interfascicular nucleus raphe IF Gad2-IRES-Cre 164985329 -3.52 0.08 4.30 0 Interfascicular nucleus raphe IF Slc17a6-IRESCre 287808449 -3.52 0.08 4.30 0 Intergeniculate leaflet of the lateral geniculate complex IGL Gad2-IRES-Cre 293942897 -2.30 2.55 3.00 0 Intergeniculate leaflet of the lateral geniculate complex IGL Plxnd1-Cre 301991713 -2.00 2.15 2.60 0 Intermediate reticular nucleus IRN C57BL/6J 126189322 -6.64 1.25 4.60 0 Intermediate reticular nucleus IRN C57BL/6J 126709328 -6.64 1.25 4.00 0 Intermediate reticular nucleus IRN C57BL/6J 127041126 0.00 calamus (-7.32 bregma) 1.00 1.36 0 Intermediate reticular nucleus IRN C57BL/6J 158838128 -5.34 0.65 4.07 0 Intermediate reticular nucleus IRN C57BL/6J 159021559 -0.24 calamus (-7.56 bregma) 1.12 2.28 0 Intermediate reticular nucleus IRN C57BL/6J 159024474 -0.24 calamus (-7.56 bregma) 1.35 1.35 0 Intermediate reticular nucleus IRN C57BL/6J 175265301 -5.34 0.65 4.10 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 36 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Intermediate reticular nucleus IRN Dbh-Cre_KH212 287029186 -6.48 1.00 4.90 0 Intermediate reticular nucleus IRN Plxnd1-Cre 301464820 -6.00 1.15 4.57 0 Intermediate reticular nucleus IRN Pnmt-Cre 156253662 -6.24 0.85 4.30 0 Intermediate reticular nucleus IRN Slc17a6-IRESCre 302016107 -6.24 0.85 4.40 0 Intermediate reticular nucleus IRN Slc18a2Cre_OZ14 265633461 -0.24 calamus (-7.56 bregma) 1.25 1.45 0 Intermediate reticular nucleus IRN Slc6a5Cre_KF109 160153696 -5.34 1.11 4.80 0 Intermediodorsal nucleus of the thalamus IMD Grm2-Cre_MR90 182185289 -1.70 0.20 3.25 0 Intermediodorsal nucleus of the thalamus IMD Lypd6Cre_KL156 298001595 -1.70 0.20 3.25 0 Intermediodorsal nucleus of the thalamus IMD Plxnd1-Cre 293365328 -1.06 0.20 3.40 0 Intermediodorsal nucleus of the thalamus IMD Syt17-Cre_NO14 286646170 -1.06 0.20 3.40 0 Intermediodorsal nucleus of the thalamus IMD Ucn3-Cre_KF43 179902786 -1.06 1.15 3.35 20 Interpeduncular nucleus IPN C57BL/6J 175158844 -3.45 0.15 4.30 0 Interpeduncular nucleus IPN Drd3-Cre_KI196 304859407 -2.70 0.13 5.20 0 Interpeduncular nucleus IPN Gad2-IRES-Cre 303474463 -3.52 0.08 4.30 0 Interpeduncular nucleus IPN Nos1-CreERT2 299761999 -3.52 0.08 4.30 0 Interpeduncular nucleus IPN Ntrk1-IRES-Cre 184212995 -3.52 0.08 4.30 0 Interpeduncular nucleus IPN Slc32a1-IRESCre 171019710 -3.52 0.08 4.30 0 Interposed nucleus IP C57BL/6J 120493315 -6.24 1.50 2.25 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 37 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Interposed nucleus IP Gabrr3Cre_KC112 168664192 -5.20 1.25 2.80 0 Interposed nucleus IP Gad2-IRES-Cre 293550435 -6.24 1.50 2.60 0 Interposed nucleus IP Gpr26Cre_KO250 265928489 -6.24 1.50 2.60 0 Interposed nucleus IP Gpr26Cre_KO250 304996627 -5.88 2.25 2.19 0 Interposed nucleus IP Ntsr1Cre_GN220 264096952 -6.24 1.50 2.60 0 Interposed nucleus IP Slc17a6-IRESCre 304474221 -6.24 1.50 2.60 0 Interposed nucleus IP Slc32a1-IRESCre 304537794 -6.24 1.50 2.60 0 Lateral amygdalar nucleus LA C57BL/6J 120762196 -1.46 3.75 3.40 0 Lateral amygdalar nucleus LA Cux2-CreERT2 310437091 -1.46 3.75 3.40 0 Lateral amygdalar nucleus LA Gad2-IRES-Cre 293975337 -1.46 3.55 3.70 0 Lateral amygdalar nucleus LA Ppp1r17Cre_NL146 287027773 -1.46 3.55 3.70 0 Lateral dorsal nucleus of thalamus LD C57BL/6J 113784293 -1.22 1.25 2.44 0 Lateral dorsal nucleus of thalamus LD C57BL/6J 272967913 -1.82 1.25 2.50 0 Lateral dorsal nucleus of thalamus LD C57BL/6J 272969333 -1.22 1.25 2.45 0 Lateral dorsal nucleus of thalamus LD Calb2-IRES-Cre 298833033 -0.94 1.12 2.60 0 Lateral dorsal nucleus of thalamus LD Gal-Cre_KI87 113554008 -1.22 1.25 2.44 0 Lateral dorsal nucleus of thalamus LD Prkcd-GluClaCFP-IRES-Cre 267609756 -0.58 1.00 2.93 0 Lateral dorsal nucleus of thalamus LD Slc17a7-IRES2Cre 301618828 -2.00 2.15 2.60 0 Lateral habenula LH C57BL/6J 147353537 -1.70 0.42 2.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 38 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral habenula LH Calb2-IRES-Cre 301057735 -1.58 0.68 2.75 0 Lateral habenula LH Grm2-Cre_MR90 292623457 -1.34 0.40 2.70 0 Lateral habenula LH Grm2-Cre_MR90 300236056 -1.70 0.42 2.45 0 Lateral hypothalamic area LHA C57BL/6J 112228391 -1.46 0.10 5.90 0 Lateral hypothalamic area LHA C57BL/6J 112372418 -0.58 3.40 4.94 40 Lateral hypothalamic area LHA C57BL/6J 112425523 -2.30 0.25 4.37 0 Lateral hypothalamic area LHA C57BL/6J 113313632 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA C57BL/6J 113369603 -0.70 1.13 5.40 0 Lateral hypothalamic area LHA C57BL/6J 114046440 -1.34 0.95 4.55 0 Lateral hypothalamic area LHA C57BL/6J 117302771 -0.58 1.75 4.50 0 Lateral hypothalamic area LHA C57BL/6J 127470271 -1.94 0.90 5.00 0 Lateral hypothalamic area LHA C57BL/6J 158258062 -1.46 0.39 5.50 0 Lateral hypothalamic area LHA C57BL/6J 158373181 -0.58 1.75 4.50 0 Lateral hypothalamic area LHA Calb2-IRES-Cre 267213087 -0.94 1.10 4.88 0 Lateral hypothalamic area LHA Crh-IRES-Cre (ZJH) 171068025 0.38 0.50 3.90 0 Lateral hypothalamic area LHA Esr1-2A-Cre 176887774 -1.50 0.78 5.75 0 Lateral hypothalamic area LHA Fezf1-2A-dCre 287667137 -1.06 1.70 5.55 0 Lateral hypothalamic area LHA Hcrt-Cre 298048079 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA Hcrt-Cre 298048787 -1.94 0.90 5.00 0 Lateral hypothalamic area LHA Lepr-IRES-Cre 113225519 -1.34 1.00 4.84 0 Lateral hypothalamic area LHA Lepr-IRES-Cre 160296448 -1.90 0.25 5.40 0 Lateral hypothalamic area LHA Lypd6Cre_KL156 298078515 -2.80 0.80 5.15 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 39 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral hypothalamic area LHA Lypd6Cre_KL156 298104533 -2.46 1.00 5.30 0 Lateral hypothalamic area LHA Oxt-IRES-Cre 113037759 -0.70 1.13 5.23 0 Lateral hypothalamic area LHA Oxt-IRES-Cre 265125894 -0.58 1.15 5.50 0 Lateral hypothalamic area LHA Plxnd1-Cre 293368154 -2.46 0.55 5.65 0 Lateral hypothalamic area LHA Pmch-Cre 113444277 -1.34 1.00 4.95 0 Lateral hypothalamic area LHA Pmch-Cre 113506174 -1.06 1.20 5.00 0 Lateral hypothalamic area LHA Pmch-Cre 142653395 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA Pmch-Cre 171020416 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA Ppp1r17Cre_NL146 267928135 -1.34 1.00 4.84 0 Lateral hypothalamic area LHA Ppp1r17Cre_NL146 278508779 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA Ppp1r17Cre_NL146 278510197 -0.94 1.10 4.88 0 Lateral hypothalamic area LHA Ppp1r17Cre_NL146 286882342 -1.50 0.35 5.30 0 Lateral hypothalamic area LHA Sim1-Cre 156195758 -1.94 0.90 5.00 0 Lateral hypothalamic area LHA Sim1-Cre 165035106 -1.34 1.00 4.84 0 Lateral hypothalamic area LHA Sim1-Cre 170860092 -0.70 1.12 5.00 0 Lateral hypothalamic area LHA Sim1-Cre 177890956 -0.58 0.20 4.75 0 Lateral hypothalamic area LHA Slc32a1-IRESCre 304674547 -1.34 1.00 4.84 0 Lateral hypothalamic area LHA Tac2-IRES2-Cre 293254286 -0.46 1.25 4.88 0 Lateral hypothalamic area LHA Tac2-IRES2-Cre 300927483 -1.50 0.35 5.30 0 Lateral posterior nucleus of the thalamus LP C57BL/6J 113846682 -3.16 2.10 2.85 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 40 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral posterior nucleus of the thalamus LP C57BL/6J 114399224 -2.18 1.45 2.44 0 Lateral posterior nucleus of the thalamus LP C57BL/6J 266585624 -1.82 1.25 2.60 0 Lateral posterior nucleus of the thalamus LP C57BL/6J 272873704 -3.16 2.05 2.65 0 Lateral posterior nucleus of the thalamus LP Calb2-IRES-Cre 183282261 -1.22 1.25 2.44 0 Lateral posterior nucleus of the thalamus LP Calb2-IRES-Cre 183282970 -2.18 1.45 2.44 0 Lateral posterior nucleus of the thalamus LP Grik4-Cre 167439900 -2.18 1.45 2.44 0 Lateral posterior nucleus of the thalamus LP Grik4-Cre 183175010 -2.18 1.45 2.44 0 Lateral posterior nucleus of the thalamus LP Nos1-CreERT2 293888501 -3.16 2.10 2.85 0 Lateral posterior nucleus of the thalamus LP Plxnd1-Cre 301466249 -2.30 2.00 2.60 0 Lateral posterior nucleus of the thalamus LP Prkcd-GluClaCFP-IRES-Cre 267608343 -1.22 1.25 2.44 0 Lateral posterior nucleus of the thalamus LP Prkcd-GluClaCFP-IRES-Cre 292319865 -2.30 2.00 2.60 0 Lateral posterior nucleus of the thalamus LP Vipr2-Cre_KE2 182805258 -3.16 2.10 2.85 0 Lateral preoptic area LPO C57BL/6J 113553300 0.62 1.20 4.85 0 Lateral preoptic area LPO C57BL/6J 113554719 0.50 0.81 4.84 0 Lateral preoptic area LPO C57BL/6J 113783321 1.18 0.60 4.15 0 Lateral preoptic area LPO C57BL/6J 146470726 -2.80 4.40 2.25 0 Lateral preoptic area LPO C57BL/6J 175263771 0.50 0.80 5.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 41 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral preoptic area LPO Crh-IRES-Cre (BL) 293114113 -4.36 0.30 4.55 0 Lateral preoptic area LPO Ntrk1-IRES-Cre 292961470 0.50 0.90 4.85 0 Lateral preoptic area LPO Ntrk1-IRES-Cre 309794438 0.74 0.50 4.25 0 Lateral preoptic area LPO Slc17a6-IRESCre 293942188 0.50 0.81 4.84 0 Lateral reticular nucleus, magnocellular part LRNm Crh-IRES-Cre (BL) 277906744 -0.34 calamus (-7.64 bregma) 1.15 2.30 0 Lateral reticular nucleus, magnocellular part LRNm Pvalb-IRES-Cre 286725359 -0.24 calamus (-7.56 Bregma) 1.12 2.30 0 Lateral reticular nucleus, magnocellular part LRNm Scnn1a-Tg2-Cre 263553934 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Lateral reticular nucleus, magnocellular part LRNm Th-Cre_FI172 304969906 -0.24 calamus (-7.56 Bregma) 1.12 2.30 0 Lateral septal nucleus LS C57BL/6J 272917631 0.38 0.30 2.30 0 Lateral septal nucleus LS Efr3aCre_NO108 300164356 0.86 0.45 2.91 0 Lateral septal nucleus, caudal (caudodorsal) part LSc Slc18a2Cre_OZ14 301672044 0.38 0.30 2.30 0 Lateral septal nucleus, caudal (caudodorsal) part LSc Sst-Cre-D 160294327 0.38 0.30 2.30 0 Lateral septal nucleus, caudal (caudodorsal) part LSc Sst-IRES-Cre 300841699 0.38 0.30 2.30 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 42 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral septal nucleus, rostral (rostroventral) part LSr C57BL/6J 100141435 0.86 0.45 2.91 0 Lateral septal nucleus, rostral (rostroventral) part LSr C57BL/6J 120436988 0.38 0.30 2.30 0 Lateral septal nucleus, rostral (rostroventral) part LSr Cart-Tg1-Cre 178486024 -1.50 0.35 5.20 0 Lateral septal nucleus, rostral (rostroventral) part LSr Gnrh1-Cre 160398593 0.98 0.25 4.60 0 Lateral septal nucleus, rostral (rostroventral) part LSr Ppp1r17Cre_NL146 267810394 0.86 0.45 2.91 0 Lateral septal nucleus, rostral (rostroventral) part LSr Prkcd-GluClaCFP-IRES-Cre 265946352 0.86 0.45 2.91 0 Lateral septal nucleus, rostral (rostroventral) part LSr Slc18a2Cre_OZ14 301672755 0.86 0.45 2.91 0 Lateral septal nucleus, rostral (rostroventral) part LSr Th-Cre_FI172 287533790 1.18 0.60 4.15 0 Lateral septal nucleus, ventral part LSv Calb2-IRES-Cre 182887258 0.10 0.40 3.67 0 Lateral vestibular nucleus LAV C57BL/6J 277618054 -6.00 1.40 3.20 0 Lateral vestibular nucleus LAV Slc17a6-IRESCre 300687607 -6.48 1.25 3.25 0 Lateral visual area VISl A930038C07RikTg1-Cre 166461899 -4.16 3.75 0.81 0 Lateral visual area VISl A930038C07RikTg1-Cre 264630019 -4.16 3.95 0.85 0 Lateral visual area VISl C57BL/6J 100141796 -4.04 4.00 0.35, 0.75 0 Lateral visual area VISl C57BL/6J 112373830 -4.60 3.80 0.45 30 Lateral visual area VISl Chrna2Cre_OE25 299782273 -4.04 4.00 0.35, 0.75 30 Lateral visual area VISl Cux2-IRES-Cre 272736450 -4.16 3.95 0.85 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 43 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lateral visual area VISl Nr5a1-Cre 286554724 -4.04 4.00 0.35, 0.75 30 Lateral visual area VISl Ntsr1Cre_GN220 159320367 -4.16 3.75 0.81 0 Lateral visual area VISl Scnn1a-Tg3-Cre 184075100 -4.04 4.00 0.35, 0.75 20 Lateral visual area VISl Syt6-Cre_KI148 267031577 -4.04 3.80 1.90 0 Laterodorsal tegmental nucleus LDT Slc18a2Cre_OZ14 301671287 -5.34 0.50 2.70 0 Lobule II CENT2 C57BL/6J 119848249 -5.68 0.50 2.32 0 Lobule II CENT2 C57BL/6J 146012184 -5.20 0.17 2.70 0 Lobule II CENT2 C57BL/6J 147134401 -5.40 0.68 2.75 0 Lobule II CENT2 C57BL/6J 156872043 -5.40 0.50 2.75 0 Lobule III CENT3 C57BL/6J 127398177 -5.68 0.50 1.45 0 Lobule III CENT3 Nxph4-2ACreERT2 287713485 -6.36 0.75 2.10 0 Lobule III CENT3 Pcp2Cre_GN135 147708352 -6.24 0.50 0.94 0 Lobule III CENT3 Slc17a6-IRESCre 304543821 -6.36 0.75 2.10 0 Lobule IV CUL4 Scnn1a-Tg3-Cre 113888575 -4.48 2.40 2.70 0 Lobule IV CUL4 Scnn1a-Tg3-Cre 156255078 -4.60 2.40 2.55 0 Lobules IV-V CUL4,5 C57BL/6J 112424102 -6.24 0.50 0.94 0 Lobules IV-V CUL4,5 C57BL/6J 114473794 -5.90 0.50 0.40 0 Lobules IV-V CUL4,5 Efr3aCre_NO108 299732033 -5.20 1.95 2.85 0 Lobules IV-V CUL4,5 Gabra6-IRESCre 181128406 -6.24 0.50 0.94 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 44 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Lobules IV-V CUL4, 5 Gad2-IRES-Cre 287809155 -6.36 0.75 2.10 0 Lobules IV-V CUL4, 5 Grm2-Cre_MR90 292531359 -6.24 0.50 0.94 0 Lobules IV-V CUL4,5 Pvalb-IRES-Cre 167202174 -6.24 0.50 0.94 0 Locus ceruleus LC C57BL/6J 277618762 -5.52 1.20 3.00 0 Locus ceruleus LC Dbh-Cre_KH212 159510205 -5.52 0.88 2.71 0 Locus ceruleus LC Dbh-Cre_KH212 159942862 -5.20 0.91 3.09 0 Locus ceruleus LC Gal-Cre_KI87 301210208 -5.52 0.88 2.71 0 Magnocellular nucleus MA Chat-IRES-Cre 161460864 0.62 1.20 4.85 0 Magnocellular nucleus MA Gad2-IRES-Cre 302736304 0.62 1.20 4.85 0 Magnocellular reticular nucleus MARN C57BL/6J 121145750 -5.88 2.25 5.00 25 Magnocellular reticular nucleus MARN C57BL/6J 127349111 0.00 calamus (-7.32 bregma) 0.85 2.05 0 Magnocellular reticular nucleus MARN Gad2-IRES-Cre 302222934 -5.88 2.25 5.30 25 Magnocellular reticular nucleus MARN Gal-Cre_KI87 178283952 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Magnocellular reticular nucleus MARN Pvalb-IRES-Cre 278066728 -5.02 0.50 5.70 0 Magnocellular reticular nucleus MARN Slc32a1-IRESCre 286647583 -5.02 0.50 5.70 0 Magnocellular reticular nucleus MARN Slc6a5Cre_KF109 160080778 -5.02 0.50 5.30 0 Main olfactory bulb MOB A930038C07RikTg1-Cre 264631432 4.28 1.20 0.70 0 Main olfactory bulb MOB C57BL/6J 100141222 4.28 0.50 2.31 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 45 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Main olfactory bulb MOB Cdhr1-Cre_KG66 146859480 4.28 0.50 2.31 0 Main olfactory bulb MOB Cdhr1-Cre_KG66 146921849 4.28 1.20 0.70 0 Main olfactory bulb MOB Cdhr1-Cre_KG66 175728165 3.08 0.45 2.55 0 Main olfactory bulb MOB Cdhr1-Cre_KG66 175731154 3.08 1.00 1.75 0 Main olfactory bulb MOB Gpr26Cre_KO250 304947087 4.28 0.50 2.31 0 Main olfactory bulb MOB Slc17a6-IRESCre 300644693 4.28 0.50 2.31 0 Main olfactory bulb MOB Slc6a3-Cre 166154193 4.28 0.50 2.31 0 Main olfactory bulb MOB Slc6a3-Cre 166156241 4.28 1.20 0.70 0 Main olfactory bulb MOB Slc6a3-Cre 182042349 3.08 0.45 2.55 0 Main olfactory bulb MOB Syt6-Cre_KI148 179642401 2.68 0.45 1.46 0 Medial amygdalar nucleus MEA C57BL/6J 146985623 -0.82 2.20 5.53 0 Medial amygdalar nucleus MEA Cart-Tg1-Cre 182041643 -0.94 1.88 5.20 0 Medial amygdalar nucleus MEA Crh-IRES-Cre (ZJH) 204907355 -1.58 2.60 3.90 0 Medial amygdalar nucleus MEA Etv1-CreERT2 267813932 -1.22 2.34 4.75 0 Medial amygdalar nucleus MEA Fezf1-2A-dCre 267547788 -1.06 1.70 5.55 0 Medial amygdalar nucleus MEA Htr2aCre_KM207 293469501 -0.94 1.88 5.20 0 Medial amygdalar nucleus MEA Sim1-Cre 170860801 -1.06 1.70 5.55 0 Medial amygdalar nucleus, anterodorsal part MEAad C57BL/6J 157550122 -0.70 2.00 5.20 0 Medial amygdalar nucleus, anterodorsal part MEAad C57BL/6J 180981417 -0.70 2.20 5.00 0 Medial amygdalar nucleus, anterodorsal part MEAad Cart-Tg1-Cre 168363874 -1.22 2.34 4.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 46 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Medial amygdalar nucleus, anterodorsal part MEAad Nos1-CreERT2 304694870 -0.94 1.88 5.20 0 Medial amygdalar nucleus, anterodorsal part MEAad Sim1-Cre 165034344 -1.22 2.34 4.75 0 Medial amygdalar nucleus, anteroventral part MEAav Adcyap1-2A-Cre 272819994 -1.06 1.70 5.55 0 Medial amygdalar nucleus, anteroventral part MEAav C57BL/6J 125361005 -0.94 1.88 5.20 0 Medial amygdalar nucleus, anteroventral part MEAav Fezf1-2A-dCre 309386361 -1.06 1.70 5.55 0 Medial amygdalar nucleus, anteroventral part MEAav Htr3aCre_NO152 305645132 -1.06 1.70 5.55 0 Medial amygdalar nucleus, posterodorsal part MEApd Crh-IRES-Cre (BL) 277856332 -1.82 2.65 4.25 0 Medial amygdalar nucleus, posterodorsal part MEApd Slc6a3-Cre 286303000 -1.22 2.34 4.75 0 Medial amygdalar nucleus, posteroventral part MEApv Sim1-Cre_KJ18 299896150 -1.58 1.80 5.45 0 Medial geniculate complex MG C57BL/6J 180520257 -3.28 2.00 2.80 0 Medial geniculate complex MG Etv1-CreERT2 113165340 -3.16 2.00 2.79 0 Medial geniculate complex MG Gal-Cre_KI87 183329991 -2.30 2.00 2.60 0 Medial geniculate complex MG Slc17a6-IRESCre 305269070 -3.16 2.10 2.85 0 Medial geniculate complex, dorsal part MGd Calb2-IRES-Cre 267493760 -2.30 2.00 2.60 0 Medial geniculate complex, ventral part MGv Calb2-IRES-Cre 299996344 -3.64 2.40 2.90 0 Medial geniculate complex, ventral part MGv Prkcd-GluClaCFP-IRES-Cre 178489574 -3.52 2.50 3.50 0 Medial habenula MH Chat-IRES-Cre 268321927 -1.70 0.42 2.45 0 Medial habenula MH Tac1-IRES2-Cre 300843826 -1.70 0.42 2.45 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 47 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Medial habenula MH Tac2-IRES2-Cre 265287564 -1.58 1.00 2.90 0 Medial mammillary nucleus MM Adcyap1-2A-Cre 307655867 -2.70 0.13 5.20 0 Medial mammillary nucleus MM C57BL/6J 148197327 -2.46 0.55 5.65 0 Medial mammillary nucleus MM Cart-Tg1-Cre 168364580 -2.35 0.13 5.10 0 Medial mammillary nucleus MM Grm2-Cre_MR90 287173396 -2.70 0.13 5.20 0 Medial mammillary nucleus MM Sim1-Cre 127396760 -2.30 0.50 5.20 0 Medial preoptic area MPO Adcyap1-2A-Cre 287246555 0.26 0.04 4.85 0 Medial preoptic area MPO C57BL/6J 119846838 0.26 0.35 4.60 0 Medial preoptic area MPO C57BL/6J 120280191 0.26 0.35 4.60 0 Medial preoptic area MPO C57BL/6J 127909584 0.46 0.50 4.80 0 Medial preoptic area MPO C57BL/6J 146660293 0.50 0.81 4.84 0 Medial preoptic area MPO C57BL/6J 158315810 0.50 0.81 4.84 0 Medial preoptic area MPO C57BL/6J 158738180 0.40 0.70 5.00 0 Medial preoptic area MPO Calb2-IRES-Cre 301061596 0.26 0.35 4.60 0 Medial preoptic area MPO Gad2-IRES-Cre 305270515 0.26 0.35 4.60 0 Medial preoptic area MPO Gal-Cre_KI87 182459635 0.26 0.04 4.85 0 Medial preoptic area MPO Ntrk1-IRES-Cre 277800288 0.98 0.15 4.65 0 Medial preoptic area MPO Slc17a6-IRESCre 292123352 0.38 0.70 5.00 0 Medial preoptic nucleus MPN C57BL/6J 126116142 0.38 0.70 5.00 0 Medial preoptic nucleus MPN Gad2-IRES-Cre 293549729 0.50 0.15 4.75 0 Medial preoptic nucleus MPN Gal-Cre_KI87 182460343 0.02 0.25 4.90 0 Medial preoptic nucleus MPN Kiss1-Cre 301989585 0.50 0.15 4.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 48 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Medial preoptic nucleus MPN Tac1-IRES2-Cre 294355509 0.26 0.35 4.60 0 Medial pretectal area MPT C57BL/6J 156979283 -2.80 0.25 2.40 0 Medial pretectal area MPT Gad2-IRES-Cre 168361750 -2.30 0.25 5.85 0 Medial septal nucleus MS C57BL/6J 100141597 0.62 0.02 3.40 0 Medial septal nucleus MS C57BL/6J 158257355 1.10 0.25 4.60 0 Medial septal nucleus MS Chat-IRES-Cre 156819600 0.62 0.02 3.40 0 Medial septal nucleus MS Drd3-Cre_KI196 298835859 1.70 0.65 4.03 0 Medial septal nucleus MS Gad2-IRES-Cre 303580293 0.62 0.02 3.40 0 Medial septal nucleus MS Gal-Cre_KI87 113696423 0.62 0.02 3.40 0 Medial septal nucleus MS Gnrh1-Cre 168094300 0.62 0.02 3.40 0 Medial septal nucleus MS Htr2aCre_KM207 293434703 1.18 0.25 3.41 0 Medial septal nucleus MS Ntrk1-IRES-Cre 265944939 0.62 0.02 3.40 0 Medial septal nucleus MS Oxtr-Cre_ON66 278259822 0.62 0.01 3.40 0 Medial vestibular nucleus MV C57BL/6J 121146455 -6.12 0.85 3.50 0 Medial vestibular nucleus MV Chrna2Cre_OE25 303709219 -6.36 0.25 3.55 0 Medial vestibular nucleus MV Ntrk1-IRES-Cre 292960764 -6.12 0.85 3.50 0 Medial vestibular nucleus MV Pnmt-Cre 143512399 -6.12 0.85 3.75 0 Medial vestibular nucleus MV Slc6a5Cre_KF109 157911126 -6.12 0.85 3.50 0 Medial vestibular nucleus MV Sst-IRES-Cre 300842406 -6.12 0.85 3.50 0 Mediodorsal nucleus of thalamus MD C57BL/6J 114291646 -0.58 0.50 3.43 0 Mediodorsal nucleus of thalamus MD C57BL/6J 156931568 -1.06 1.75 3.15 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 49 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Mediodorsal nucleus of thalamus MD C57BL/6J 173206592 -0.70 0.70 2.80 0 Mediodorsal nucleus of thalamus MD C57BL/6J 267494468 -1.94 0.50 3.20 0 Mediodorsal nucleus of thalamus MD C57BL/6J 272830456 -0.58 0.62 2.92 0 Mediodorsal nucleus of thalamus MD C57BL/6J 272875132 -1.06 1.15 3.35 20 Mediodorsal nucleus of thalamus MD C57BL/6J 272875838 -1.34 0.40 2.70 0 Mediodorsal nucleus of thalamus MD C57BL/6J 272970747 -1.46 0.10 3.35 0 Mediodorsal nucleus of thalamus MD Calb2-IRES-Cre 183329222 -1.34 0.50 3.40 0 Mediodorsal nucleus of thalamus MD Calb2-IRES-Cre 301060890 -1.34 0.50 3.40 0 Mediodorsal nucleus of thalamus MD Gal-Cre_KI87 116904684 -1.34 0.50 3.40 0 Mediodorsal nucleus of thalamus MD Gal-Cre_KI87 168002780 -0.70 0.60 2.90 0 Mediodorsal nucleus of thalamus MD Grik4-Cre 168300739 -1.46 0.44 3.20 0 Mediodorsal nucleus of thalamus MD Grik4-Cre 168301446 -0.82 0.25 2.80 0 Mediodorsal nucleus of thalamus MD Grp-Cre_KH288 183058837 -1.58 0.68 2.73 0 Mediodorsal nucleus of thalamus MD Ppp1r17Cre_NL146 268399145 -0.82 0.25 2.80 0 Mediodorsal nucleus of thalamus MD Ppp1r17Cre_NL146 278400363 -1.46 0.44 3.20 0 Mediodorsal nucleus of thalamus MD Prkcd-GluClaCFP-IRES-Cre 267607635 -1.46 0.44 3.20 0 Mediodorsal nucleus of thalamus MD Prkcd-GluClaCFP-IRES-Cre 267928844 -0.82 0.25 2.80 0 Mediodorsal nucleus of thalamus MD Slc17a6-IRESCre 181895006 -0.70 0.60 2.90 0 Mediodorsal nucleus of thalamus MD Slc17a6-IRESCre 294356922 -1.34 0.50 3.40 0 Mediodorsal nucleus of thalamus MD Syt17-Cre_NO14 286485585 -0.70 0.60 3.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 50 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Mediodorsal nucleus of thalamus MD Tac1-IRES2-Cre 300889379 -1.06 1.15 3.35 20 Mediodorsal nucleus of thalamus MD Vipr2-Cre_KE2 268076421 -1.34 0.50 3.40 0 Medullary reticular nucleus, ventral part MDRNv C57BL/6J 127353220 -0.24 calamus (-7.56 bregma) 1.25 1.43 0 Medullary reticular nucleus, ventral part MDRNv C57BL/6J 273068974 -0.24 calamus (-7.56 bregma) 0.95 2.30 0 Medullary reticular nucleus, ventral part MDRNv Slc17a6-IRESCre 302085421 -6.48 1.00 4.90 0 Midbrain reticular nucleus MRN C57BL/6J 113399428 -3.64 1.50 2.96 0 Midbrain reticular nucleus MRN C57BL/6J 114474520 -3.64 1.50 2.60 0 Midbrain reticular nucleus MRN C57BL/6J 120760759 -3.80 0.87 3.30 0 Midbrain reticular nucleus MRN C57BL/6J 126352037 -4.16 1.00 2.65 0 Midbrain reticular nucleus MRN C57BL/6J 127557915 -3.88 1.30 3.45 0 Midbrain reticular nucleus MRN C57BL/6J 127865687 -3.28 0.60 3.65 0 Midbrain reticular nucleus MRN C57BL/6J 127991964 -4.04 1.80 2.73 0 Midbrain reticular nucleus MRN C57BL/6J 139311530 -3.28 0.91 3.10 0 Midbrain reticular nucleus MRN C57BL/6J 147354242 -2.18 0.80 3.20 0 Midbrain reticular nucleus MRN C57BL/6J 156978574 -4.04 1.80 2.73 0 Midbrain reticular nucleus MRN C57BL/6J 174583904 -2.30 0.60 3.50 0 Midbrain reticular nucleus MRN C57BL/6J 273065264 -3.88 1.30 3.55 0 Midbrain reticular nucleus MRN Erbb4-2ACreERT2 180522266 -3.28 0.36 4.13 0 Midbrain reticular nucleus MRN Gad2-IRES-Cre 287598261 -3.80 0.04 2.85 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 51 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Midbrain reticular nucleus MRN Gad2-IRES-Cre 302723204 -3.28 0.60 3.65 0 Midbrain reticular nucleus MRN Htr2aCre_KM207 278401778 -2.92 1.25 2.76 0 Midbrain reticular nucleus MRN Pvalb-IRES-Cre 258914806 -3.28 0.60 3.65 0 Midbrain reticular nucleus MRN Th-Cre_FI172 304761539 -3.08 1.25 4.15 0 Midbrain trigeminal nucleus MEV Pvalb-IRES-Cre 267030155 -4.36 0.70 2.20 0 Motor nucleus of trigeminal V Chat-IRES-Cre 166052101 -5.20 1.35 3.10 0 Motor nucleus of trigeminal V Pcdh9-Cre 272829024 -5.20 1.40 3.55 0 Motor nucleus of trigeminal V Pvalb-IRES-Cre 182804552 -4.36 1.60 4.27 0 Motor nucleus of trigeminal V Scnn1a-Tg2-Cre 162019589 -5.20 1.40 3.31 0 Nodulus (X) NOD C57BL/6J 120874405 -6.64 0.50 2.55 0 Nodulus (X) NOD Gad2-IRES-Cre 305293222 -6.12 0.85 3.50 0 Nucleus accumbens ACB C57BL/6J 127255254 1.70 0.80 3.40 0 Nucleus accumbens ACB C57BL/6J 146045723 1.54 1.13 4.85 0 Nucleus accumbens ACB C57BL/6J 175373569 1.18 1.25 3.90 0 Nucleus accumbens ACB Calb2-IRES-Cre 264874516 2.10 0.75 4.05 0 Nucleus accumbens ACB Drd1a-Cre 168614604 1.18 0.60 4.15 0 Nucleus accumbens ACB Drd1a-Cre 168615344 1.70 0.80 3.40 0 Nucleus accumbens ACB Drd1a-Cre 170785775 1.54 1.13 4.85 0 Nucleus accumbens ACB Drd2-Cre_ER44 158020947 1.18 1.25 3.80 0 Nucleus accumbens ACB Drd2-Cre_ER44 167904966 1.54 1.13 4.85 0 Nucleus accumbens ACB Drd2-Cre_ER44 175732001 1.70 0.65 4.00 0 Nucleus accumbens ACB Drd3-Cre_KI196 300078901 0.86 0.50 3.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 52 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Nucleus accumbens ACB Drd3-Cre_KI196 300110369 -0.10 2.55 4.00 30 Nucleus accumbens ACB Gpr26Cre_KO250 286486329 2.10 0.75 4.20 0 Nucleus accumbens ACB Kcnc2-Cre 171411651 2.34 0.40 4.00 0 Nucleus accumbens ACB Ntrk1-IRES-Cre 265136608 1.18 0.60 4.15 0 Nucleus accumbens ACB Ntrk1-IRES-Cre 287993060 1.70 0.65 4.03 0 Nucleus ambiguus AMB Chat-IRES-Cre 264321572 -0.24 calamus (-7.56 bregma) 1.25 1.45 0 Nucleus accumbens ACB Ntrk1-IRES-Cre 293008559 1.10 1.50 5.15 0 Nucleus accumbens ACB Ntrk1-IRES-Cre 309739641 1.18 1.25 3.80 0 Nucleus accumbens ACB Ntrk1-IRES-Cre 309740347 1.70 0.80 3.40 0 Nucleus incertus NI Ntrk1-IRES-Cre 265930674 -4.84 0.22 3.75 0 Nucleus incertus NI Ntrk1-IRES-Cre 277799582 -4.84 0.22 3.75 0 Nucleus of Darkschewitsch ND Pdzk1ip1Cre_KD31 267029447 -3.28 0.20 3.10 0 Nucleus of reunions RE Adcyap1-2A-Cre 204832205 -0.58 0.17 4.40 0 Nucleus of reunions RE C57BL/6J 113504763 -0.58 0.17 4.40 0 Nucleus of reunions RE C57BL/6J 174957972 -0.58 0.20 4.05 0 Nucleus of reunions RE C57BL/6J 175019536 -1.22 0.30 4.15 0 Nucleus of reunions RE C57BL/6J 175374982 -1.46 0.30 5.35 0 Nucleus of reunions RE Calb2-IRES-Cre 184158290 -0.58 0.17 4.20 0 Nucleus of reunions RE Cart-Tg1-Cre 265286700 -0.58 0.17 4.40 0 Nucleus of reunions RE Htr2aCre_KM207 278500868 -0.22 2.25 4.03 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 53 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Nucleus of reunions RE Prkcd-GluClaCFP-IRES-Cre 265947058 -0.58 0.17 4.40 0 Nucleus of reunions RE Rasgrf2-2A-dCre 310976160 -0.58 0.20 4.75 0 Nucleus of reunions RE Slc17a6-IRESCre 304617742 -0.80 0.25 4.85 0 Nucleus of reunions RE Ucn3-Cre_KF43 167025578 -0.94 0.25 4.52 0 Nucleus of the brachium of the inferior colliculus NB Pdzk1ip1Cre_KD31 159995481 -4.04 1.80 2.73 0 Nucleus of the lateral lemniscus NLL C57BL/6J 119846129 -4.60 2.40 2.55 0 Nucleus of the lateral lemniscus NLL Scnn1a-Tg3-Cre 156313344 -4.24 2.36 3.58 0 Nucleus of the lateral lemniscus NLL Sst-IRES-Cre 309385637 -3.88 1.30 3.45 0 Nucleus of the lateral lemniscus, ventral part NLLv Pdzk1ip1Cre_KD31 157766259 -4.36 1.60 4.27 0 Nucleus of the lateral olfactory tract NLOT C57BL/6J 138058320 -0.10 2.00 5.07 0 Nucleus of the lateral olfactory tract NLOT Sim1-Cre 159151138 -0.46 2.20 5.22 0 Nucleus of the lateral olfactory tract NLOT Slc17a6-IRESCre 294174996 -0.46 2.20 5.22 0 Nucleus of the optic tract NOT C57BL/6J 126523791 -2.80 1.00 2.15 0 Nucleus of the optic tract NOT C57BL/6J 158915602 -2.80 1.00 2.00 0 Nucleus of the posterior commissure NPC C57BL/6J 158737454 -2.18 0.80 3.20 0 Nucleus of the solitary tract NTS C57BL/6J 159648854 0.10 calamus (-7.10 bregma) 0.25 0.25 0 Nucleus of the solitary tract NTS Gad2-IRES-Cre 302050617 0.2 calamus (-7.00 bregma) 0.25 0.15 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 54 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Nucleus of the solitary tract NTS Gal-Cre_KI87 175816975 0.20 calamus (-7.00 bregma) 0.25 0.15 0 Nucleus of the solitary tract NTS Pnmt-Cre 155735108 0.00 calamus (-7.20 bregma) 0.25 0.15 0 Nucleus of the solitary tract NTS Rasgrf2-2A-dCre 310853453 0.20 0.25 0.15 0 Nucleus of the solitary tract NTS Slc6a5Cre_KF109 128003477 0.00 calamus (-7.20 bregma) 0.25 0.15 0 Nucleus of the solitary tract NTS Tac1-IRES2-Cre 180525136 0.20 calamus (-7.00 bregma) 0.25 0.15 0 Nucleus prepositus PRP C57BL/6J 127908173 -6.36 0.25 3.55 0 Nucleus raphe magnus RM C57BL/6J 147159899 -5.88 2.25 5.30 25 Nucleus raphe magnus RM C57BL/6J 175264587 -4.16 0.25 5.50 0 Nucleus raphe obscurus RO Crh-IRES-Cre (ZJH) 267153115 0.00 calamus (-7.32 bregma) 0.00 1.20 0 Nucleus raphe obscurus RO Crh-IRES-Cre (ZJH) 301875208 -6.64 0.78 4.80 10 Nucleus raphe obscurus RO Gal-Cre_KI87 300209456 -6.64 0.78 4.80 10 Nucleus raphe obscurus RO Slc18a2Cre_OZ14 292794673 0.00 calamus (-7.32 bregma) 0.05 1.00 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 55 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Nucleus raphe obscurus RO Slc6a4Cre_ET33 133286781 0.00 calamus (-7.32 bregma) 0.00 1.00 0 Nucleus raphe obscurus RO Slc6a4Cre_ET33 141603895 -6.64 0.78 4.80 10 Nucleus raphe obscurus RO Slc6a4CreERT2_EZ13 167212217 -6.64 0.78 4.80 10 Nucleus raphe obscurus RO Slc6a4CreERT2_EZ13 168227692 0.00 calamus (-7.32 bregma) 0.00 1.00 0 Nucleus raphe pontis RPO Cnnm2Cre_KD18 167376068 -4.72 0.25 4.40 0 Nucleus raphe pontis RPO Slc18a2Cre_OZ14 287095785 -4.84 0.22 3.75 0 Nucleus raphe pontis RPO Slc6a4Cre_ET33 267958444 -4.84 0.22 3.75 0 Oculomotor nucleus III C57BL/6J 121509005 -4.16 0.14 2.99 0 Oculomotor nucleus III Chat-IRES-Cre 177460028 -4.04 0.10 3.00 0 Oculomotor nucleus III Htr3aCre_NO152 311845265 -4.04 0.10 3.00 0 Oculomotor nucleus III Pvalb-IRES-Cre 266099165 -4.24 0.52 2.86 10 Olfactory tubercle OT C57BL/6J 114755099 2.34 0.40 4.00 0 Olfactory tubercle OT C57BL/6J 147632458 1.10 1.50 5.25 0 Olfactory tubercle OT C57BL/6J 157659671 1.54 1.15 5.00 0 Olfactory tubercle OT Drd2-Cre_ER44 167904255 1.10 1.50 5.15 0 Olfactory tubercle OT Ntrk1-IRES-Cre 292962283 1.54 1.13 4.85 0 Olivary pretectal nucleus OP C57BL/6J 113442864 -2.54 0.70 2.24 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 56 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Olivary pretectal nucleus OP Pdzk1ip1Cre_KD31 182031296 -2.35 0.70 2.24 0 Orbital area ORB Chrna2Cre_OE25 297892843 1.00 0.75 0.30, 0.75 0 Orbital area, lateral part ORBl A930038C07RikTg1-Cre 168164972 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl C57BL/6J 112306316 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Chrna2Cre_OE25 278174451 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Cux2-IRES-Cre 183471174 2.80 1.25 1.30 0 Orbital area, lateral part ORBl Efr3aCre_NO108 298230624 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Gpr26Cre_KO250 265713683 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Grm2-Cre_MR90 264708349 2.80 1.25 1.30 0 Orbital area, lateral part ORBl Grp-Cre_KH288 288324211 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Nos1-CreERT2 268319809 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Nos1-CreERT2 293889216 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Nr5a1-Cre 159887627 -2.54 1.75 0.20, 0.55 0 Orbital area, lateral part ORBl Oxtr-Cre_ON66 294311830 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Rasgrf2-2A-dCre 303783725 2.80 1.25 1.30 0 Orbital area, lateral part ORBl Rbp4-Cre_KL100 156741826 2.80 1.25 1.30, 1.67 0 Orbital area, lateral part ORBl Syt6-Cre_KI148 126353451 2.80 1.25 1.30, 1.67 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 57 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Orbital area, lateral part ORBl Tlx3-Cre_PL56 293433283 2.80 1.25 1.30, 1.67 0 Orbital area, medial part ORBm A930038C07RikTg1-Cre 283019341 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm C57BL/6J 126860974 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Chrna2Cre_OE25 298274021 2.10 0.06, 0.33 1.50 0 Orbital area, medial part ORBm Crh-IRES-Cre (BL) 277855624 2.68 0.65 1.84 0 Orbital area, medial part ORBm Cux2-IRES-Cre 272781246 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Cux2-IRES-Cre 293471629 2.68 0.05, 0.35 1.45 0 Orbital area, medial part ORBm Efr3aCre_NO108 286648290 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Gpr26Cre_KO250 301323451 2.68 0.05, 0.35 1.45 0 Orbital area, medial part ORBm Htr2aCre_KM207 258916270 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Htr2aCre_KM207 277956496 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Ntsr1Cre_GN220 159511623 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Syt6-Cre_KI148 159209586 2.68 0.05, 0.45 1.46 0 Orbital area, medial part ORBm Syt6-Cre_KI148 265820216 2.68 0.45 1.46 0 Orbital area, ventrolateral part ORBvl C57BL/6J 112423392 2.68 0.65 1.84 0 Orbital area, ventrolateral part ORBvl C57BL/6J 158435116 3.00 1.00 1.90 0 Orbital area, ventrolateral part ORBvl Grp-Cre_KH288 266564027 2.68 0.05, 0.45 1.46 0 Orbital area, ventrolateral part ORBvl Htr2aCre_KM207 183618845 2.80 1.25 1.30, 1.67 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 58 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Orbital area, ventrolateral part ORBvl Rbp4-Cre_KL100 167902586 2.68 0.05, 0.45 1.46 0 Orbital area, ventrolateral part ORBvl Rbp4-Cre_KL100 287769286 -0.10 2.55 4.00 30 Orbital area, ventrolateral part ORBvl Slc32a1-IRESCre 309580102 3.08 1.00 1.75 0 Orbital area, ventrolateral part ORBvl Sst-IRES-Cre 288263341 2.80 1.25 1.30, 1.67 0 Orbital area, ventrolateral part ORBvl Syt17-Cre_NO14 127560043 3.20 1.00 1.50 0 Parabigeminal nucleus PBG C57BL/6J 127091083 -4.16 2.25 2.27 0 Parabrachial nucleus PB Adcyap1-2A-Cre 301016900 -5.34 1.50 3.75 0 Parabrachial nucleus PB C57BL/6J 127085717 -5.52 0.88 2.71 0 Parabrachial nucleus PB C57BL/6J 127469566 -5.20 1.25 2.80 0 Parabrachial nucleus PB C57BL/6J 147635309 -4.48 1.15 3.00 0 Parabrachial nucleus PB C57BL/6J 268415561 -5.20 1.40 3.35 0 Parabrachial nucleus PB Calb2-IRES-Cre 183284388 -5.20 1.25 2.80 0 Parabrachial nucleus PB Chat-IRES-Cre 183901489 -5.52 0.88 2.71 0 Parabrachial nucleus PB Chat-IRES-Cre 264565965 -5.20 1.25 2.80 0 Parabrachial nucleus PB Gad2-IRES-Cre 303535149 -5.20 1.25 2.80 0 Parabrachial nucleus PB Grm2-Cre_MR90 292790567 -5.20 1.25 2.80 0 Parabrachial nucleus PB Grp-Cre_KH288 265487421 -5.20 1.25 2.80 0 Parabrachial nucleus PB Htr3aCre_NO152 311845972 -5.52 0.88 2.71 0 Parabrachial nucleus PB Nxph4-2ACreERT2 301991007 -5.34 0.50 2.70 0 Parabrachial nucleus PB Rasgrf2-2A-dCre 313141786 -5.52 0.88 2.71 0 Parabrachial nucleus PB Slc17a6-IRESCre 278401072 -5.02 1.20 2.30 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 59 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Parabrachial nucleus PB Slc17a6-IRESCre 305404551 -5.40 0.50 2.75 0 Parabrachial nucleus PB Syt17-Cre_NO14 167442042 -5.34 1.20 2.80 0 Parabrachial nucleus PB Tac1-IRES2-Cre 294356216 -5.20 1.25 2.80 0 Parabrachial nucleus PB Th-Cre_FI172 301016175 -5.20 1.25 2.80 0 Paracentral nucleus PCN Gal-Cre_KI87 168095041 -0.58 0.50 3.43 0 Paracentral nucleus PCN Grm2-Cre_MR90 166264185 -1.34 0.50 3.40 0 Paracentral nucleus PCN Grp-Cre_KH288 183071513 -1.34 0.50 3.40 0 Parafascicular nucleus PF C57BL/6J 266693274 -1.94 0.70 3.60 0 Parafascicular nucleus PF C57BL/6J 272968624 -1.94 0.70 3.50 0 Parafascicular nucleus PF Efr3aCre_NO108 299732738 -2.30 0.80 3.20 0 Parafascicular nucleus PF Rbp4-Cre_KL100 300642574 -2.30 0.80 3.20 0 Parafascicular nucleus PF Slc17a6-IRESCre 263785543 -2.06 0.45 4.00 0 Parafascicular nucleus PF Slc17a6-IRESCre 266412078 0.98 2.65 3.19 0 Parafascicular nucleus PF Slc17a6-IRESCre 309580808 -2.18 1.23 3.71 20 Parafascicular nucleus PF Slc18a2Cre_OZ14 301735080 -2.06 0.45 4.00 0 Parafascicular nucleus PF Vipr2-Cre_KE2 267959197 -1.58 0.68 2.73 0 Paraflocculus PFL C57BL/6J 119847544 -5.40 2.80 2.55 0 Paraflocculus PFL C57BL/6J 120438416 -5.40 2.80 2.55 0 Paraflocculus PFL C57BL/6J 158738894 -4.96 3.00 2.55 0 Paraflocculus PFL Grik4-Cre 182685522 -4.96 3.10 2.65 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 60 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Paraflocculus PFL Slc32a1-IRESCre 304675961 -6.12 2.25 2.90 0 Paragigantocellular reticular nucleus, lateral part PGRNl C57BL/6J 127042540 -0.24 calamus (-7.56 bregma) 1.12 2.28 0 Paragigantocellular reticular nucleus, lateral part PGRNl C57BL/6J 175142304 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Paragigantocellular reticular nucleus, lateral part PGRNl C57BL/6J 181058463 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Paragigantocellular reticular nucleus, lateral part PGRNl Chat-IRES-Cre 161460153 -6.48 1.00 4.82 0 Paragigantocellular reticular nucleus, lateral part PGRNl Gal-Cre_KI87 182458849 -0.24 calamus (-7.56 bregma) 1.12 2.30 0 Paragigantocellular reticular nucleus, lateral part PGRNl Scnn1a-Tg2-Cre 171409520 -0.24 calamus (-7.56 Bregma) 1.12 2.30 0 Paramedian lobule PRM C57BL/6J 125801739 -7.20 2.25 1.63 0 Parasubiculum PAR C57BL/6J 100148554 -4.48 3.00 3.44 0 Parasubiculum PAR C57BL/6J 120280939 -4.60 2.40 2.55 0 Parasubiculum PAR Cux2-CreERT2 177322126 -4.48 3.00 3.44 0 Parasubiculum PAR Nos1-CreERT2 305071285 4.60 2.40 2.55 0 Parasubiculum PAR Scnn1a-Tg3-Cre 184075807 -4.24 2.50 3.60 0 Parasubiculum PAR Wfs1-Tg2CreERT2 292530653 -4.24 2.50 3.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 61 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Parasubiculum PAR Wfs1-Tg3CreERT2 182617186 -4.24 2.36 3.58 0 Parasubthalamic nucleus PSTN A930038C07RikTg1-Cre 264696942 -2.18 1.25 4.95 0 Parasubthalamic nucleus PSTN Ucn3-Cre_KF43 165974379 -2.18 1.25 4.95 0 Parataenial nucleus PT C57BL/6J 123662982 -0.10 2.55 4.00 30 Parataenial nucleus PT C57BL/6J 126843200 -0.48 0.38 3.58 0 Parataenial nucleus PT Cart-Tg1-Cre 176897793 -0.10 2.55 4.00 30 Parataenial nucleus PT Cck-IRES-Cre 159432479 -0.34 0.35 3.58 0 Parataenial nucleus PT Crh-IRES-Cre (BL) 167373923 -0.70 0.50 3.43 0 Parataenial nucleus PT Crh-IRES-Cre (BL) 266839077 0.38 0.50 3.90 0 Parataenial nucleus PT Slc17a6-IRESCre 305125123 -0.58 0.50 3.43 0 Parataenial nucleus PT Slc17a6-IRESCre 305449231 -0.34 0.35 3.58 0 Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 183459175 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 267997620 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Avp-IRES2-Cre 287044088 -0.80 0.25 4.85 0 Paraventricular hypothalamic nucleus PVH Crh-IRES-Cre (BL) 170784358 -0.58 3.40 4.94 40 Paraventricular hypothalamic nucleus PVH Crh-IRES-Cre (BL) 266840498 -0.80 0.25 4.85 0 Paraventricular hypothalamic nucleus PVH Efr3aCre_NO108 299759881 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Gad2-IRES-Cre 294040662 0.38 0.02 4.20 0 Paraventricular hypothalamic nucleus PVH Gad2-IRES-Cre 302221478 -0.58 0.20 4.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 62 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Paraventricular hypothalamic nucleus PVH Gal-Cre_KI87 176432524 -0.94 0.25 4.80 0 Paraventricular hypothalamic nucleus PVH Nos1-CreERT2 304998039 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 112951097 -0.58 0.17 4.45 0 Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 146983504 -0.58 3.40 4.94 40 Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 147051682 -0.94 0.25 4.52 0 Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 147136518 -0.58 3.40 4.94 40 Paraventricular hypothalamic nucleus PVH Oxt-IRES-Cre 166532512 -0.94 0.25 4.80 0 Paraventricular hypothalamic nucleus PVH Sim1-Cre 241280698 0.38 0.02 4.20 0 Paraventricular hypothalamic nucleus PVH Tac1-IRES2-Cre 300888673 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Th-Cre_FI172 301014055 -0.58 0.20 4.75 0 Paraventricular hypothalamic nucleus PVH Ucn3-Cre_KF43 127470976 -0.58 3.40 4.94 40 Paraventricular nucleus of the thalamus PVT C57BL/6J 120875111 -1.58 1.00 2.90 20 Paraventricular nucleus of the thalamus PVT C57BL/6J 127255962 -1.06 1.76 3.15 30 Paraventricular nucleus of the thalamus PVT C57BL/6J 147162736 0.14 2.55 4.00 30 Paraventricular nucleus of the thalamus PVT C57BL/6J 180568155 -0.34 0.05 3.45 0 Paraventricular nucleus of the thalamus PVT C57BL/6J 272874417 -0.34 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Calb2-IRES-Cre 184157585 -1.06 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Efr3aCre_NO108 301209502 -1.06 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Gal-Cre_KI87 204908781 -0.34 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Grm2-Cre_MR90 175739791 -1.58 0.35 2.73 0 Paraventricular nucleus of the thalamus PVT Grm2-Cre_MR90 183225830 -0.34 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Ntrk1-IRES-Cre 263106751 -1.06 1.15 3.35 20 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 63 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Paraventricular nucleus of the thalamus PVT Oxtr-Cre_ON66 299448592 -1.06 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Ppp1r17Cre_NL146 278510903 -0.46 0.12 3.58 0 Paraventricular nucleus of the thalamus PVT Rasgrf2-2A-dCre 313324664 -1.06 1.15 3.35 20 Paraventricular nucleus of the thalamus PVT Syt17-Cre_NO14 299624500 -1.06 0.20 3.40 0 Parvicellular reticular nucleus PARN C57BL/6J 147354951 -5.80 1.30 4.20 0 Parvicellular reticular nucleus PARN Gad2-IRES-Cre 300208016 -5.80 1.30 4.20 0 Parvicellular reticular nucleus PARN Gad2-IRES-Cre 308981706 -5.80 1.30 4.20 0 Parvicellular reticular nucleus PARN Slc17a6-IRESCre 294173584 -6.64 1.25 4.00 0 Pedunculopontine nucleus PPN Chat-IRES-Cre 264566672 -4.48 1.15 3.50 0 Pedunculopontine nucleus PPN Lypd6Cre_KL156 298079222 -4.48 1.15 3.50 0 Pedunculopontine nucleus PPN Pvalb-IRES-Cre 293252166 -5.20 1.95 3.35 0 Periaqueductal gray PAG Adcyap1-2A-Cre 287247978 -4.24 0.52 2.86 10 Periaqueductal gray PAG C57BL/6J 113096571 -3.80 0.43 2.50 0 Periaqueductal gray PAG C57BL/6J 120761491 -5.02 0.75 1.98 0 Periaqueductal gray PAG C57BL/6J 128002057 -4.84 0.30 3.10 0 Periaqueductal gray PAG C57BL/6J 158376179 -3.52 0.08 4.30 0 Periaqueductal gray PAG C57BL/6J 272829745 -3.28 0.36 4.13 0 Periaqueductal gray PAG Cck-IRES-Cre 183562831 -4.04 0.10 3.00 0 Periaqueductal gray PAG Cck-IRES-Cre 299856390 -3.80 0.04 2.85 0 Periaqueductal gray PAG Dbh-Cre_KH212 300076066 -4.96 0.50 2.60 0 Periaqueductal gray PAG Gad2-IRES-Cre 162020630 -3.80 0.04 2.31 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 64 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Periaqueductal gray PAG Gad2-IRES-Cre 302053755 -4.36 0.50 2.01 0 Periaqueductal gray PAG Grm2-Cre_MR90 292624169 -5.02 0.75 1.98 0 Periaqueductal gray PAG Lypd6Cre_KL156 298079928 -4.96 0.50 2.60 0 Periaqueductal gray PAG Nxph4-2ACreERT2 287712779 -3.80 0.04 2.85 0 Periaqueductal gray PAG Oxtr-Cre_ON66 278261300 -2.30 0.25 3.90 0 Periaqueductal gray PAG Rbp4-Cre_KL100 301540850 -3.80 0.04 2.85 0 Periaqueductal gray PAG Rbp4-Cre_KL100 301541824 -3.80 0.04 2.85 0 Periaqueductal gray PAG Slc6a3-Cre 160538548 -4.36 0.18 2.10 0 Periaqueductal gray PAG Syt6-Cre_KI148 182144176 -1.58 1.00 2.95 20 Periaqueductal gray PAG Syt6-Cre_KI148 304949216 -4.24 0.52 2.86 10 Periaqueductal gray PAG Tac1-IRES2-Cre 180524412 -3.28 0.36 4.13 0 Periaqueductal gray PAG Th-Cre_FI172 272699357 -4.16 0.14 2.99 0 Periaqueductal gray PAG Vip-IRES-Cre 262188772 -4.24 0.52 2.86 10 Periaqueductal gray PAG Vipr2-Cre_KE2 182280207 -3.80 0.04 2.85 0 Perirhinal area PERI C57BL/6J 142656218 -4.24 4.00 1.65 0 Perirhinal area PERI C57BL/6J 180435652 -2.80 4.30 2.05 0 Periventricular hypothalamic nucleus, posterior part PVp Agrp-IRES-Cre 167117360 -1.90 0.25 5.90 0 Periventricular hypothalamic nucleus, posterior part PVp Gad2-IRES-Cre 168362462 -2.80 0.25 2.40 0 Periventricular hypothalamic nucleus, posterior part PVp Gal-Cre_KI87 168005102 -1.90 0.25 5.90 0 Periventricular hypothalamic nucleus, posterior part PVp Ins2-Cre 298178912 -1.90 0.25 5.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 65 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Periventricular hypothalamic nucleus, posterior part PVp Lepr-IRES-Cre 179904203 -2.30 0.25 5.85 0 Periventricular hypothalamic nucleus, posterior part PVp Slc32a1-IRESCre 264078267 -2.30 0.25 5.85 0 Periventricular hypothalamic nucleus, preoptic part PVpo C57BL/6J 114472860 0.26 0.04 4.85 0 Piriform area PIR A930038C07RikTg1-Cre 286775476 -0.34 4.00, 3.75 3.00, 3.25 0 Piriform area PIR Adcyap1-2A-Cre 287225747 -0.46 3.45 4.80 0 Piriform area PIR C57BL/6J 112307046 0.98 2.85 3.14 0 Piriform area PIR C57BL/6J 127907465 1.42 2.80 3.50 0 Piriform area PIR C57BL/6J 131068390 -0.58 3.65 4.10 0 Piriform area PIR C57BL/6J 146857301 -1.46 4.10 3.70 0 Piriform area PIR C57BL/6J 146984209 -1.46 3.95 3.40 0 Piriform area PIR C57BL/6J 157654069 -0.34 3.90 3.20 0 Piriform area PIR C57BL/6J 158374671 -1.46 3.75 3.70 0 Piriform area PIR Cart-Tg1-Cre 171485060 -1.46 3.55 3.70 0 Piriform area PIR Cux2-CreERT2 286728190 -0.22 3.30 3.25 0 Piriform area PIR Cux2-CreERT2 310436191 0.98 2.85 3.14 0 Piriform area PIR Cux2-CreERT2 310439724 -0.46 3.00 4.40 0 Piriform area PIR Drd3-Cre_KI196 300109663 -1.46 4.00 3.70 0 Piriform area PIR Drd3-Cre_KI198 300168916 -1.46 4.00 3.70 0 Piriform area PIR Rbp4-Cre_KL100 298720898 -1.46 4.00 3.70 0 Piriform area PIR Slc32a1-IRESCre 305294666 -1.46 4.00 3.70 0 Piriform area PIR Syt17-Cre_NO14 184259031 -1.46 4.00 3.70 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 66 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Piriform area PIR Syt6-Cre_KI148 159433905 -0.34 4.00, 3.75 3.00, 3.25 0 Piriform area PIR Vip-IRES-Cre 299655676 -1.06 3.00 3.90 0 Piriform area PIR Vip-IRES-Cre 299897573 -0.58 3.65 4.10 0 Piriform-amygdalar area PAA Gad2-IRES-Cre 302740314 -1.70 2.75 5.25 0 Pontine central gray PCG C57BL/6J 142655513 -4.48 0.12 3.77 0 Pontine central gray PCG C57BL/6J 143513811 -5.20 0.06 3.25 0 Pontine central gray PCG C57BL/6J 158434409 -5.20 0.25 4.40 0 Pontine central gray PCG C57BL/6J 158435826 -5.40 0.68 2.90 0 Pontine central gray PCG Crh-IRES-Cre (ZJH) 182224715 -5.52 0.88 2.71 0 Pontine central gray PCG Crh-IRES-Cre (ZJH) 307928463 -4.84 0.22 3.75 0 Pontine central gray PCG Ntrk1-IRES-Cre 262215150 -5.40 0.50 2.75 0 Pontine central gray PCG Sst-IRES-Cre 310377782 -5.20 0.17 3.30 0 Pontine reticular nucleus PRNr C57BL/6J 127223428 -4.36 0.30 4.35 0 Pontine reticular nucleus PRNr C57BL/6J 152995635 -4.48 0.75 4.10 0 Pontine reticular nucleus PRNr C57BL/6J 156930126 -4.36 1.70 4.35 0 Pontine reticular nucleus PRNr Crh-IRES-Cre (ZJH) 310695955 -4.72 0.25 4.40 0 Pontine reticular nucleus PRNr Pvalb-IRES-Cre 258316862 -4.60 0.50 5.30 0 Pontine reticular nucleus PRNr Slc6a5Cre_KF109 258315443 -4.36 1.60 4.27 0 Pontine reticular nucleus, caudal part PRNc C57BL/6J 125437216 -5.34 0.50 4.07 0 Pontine reticular nucleus, caudal part PRNc C57BL/6J 147633885 -5.34 0.50 4.07 0 Pontine reticular nucleus, caudal part PRNc C57BL/6J 272700063 -4.60 0.75 4.10 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 67 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Pontine reticular nucleus, caudal part PRNc C57BL/6J 272826010 -4.04 0.25 5.90 0 Pontine reticular nucleus, caudal part PRNc Slc6a5Cre_KF109 168515225 -4.48 0.75 4.10 0 Pontine reticular nucleus, caudal part PRNc Slc6a5Cre_KF109 300691325 -4.96 1.05 4.90 0 Pontine reticular nucleus, caudal part PRNc Slc17a6-IRESCre 309701202 -4.36 0.30 4.55 0 Posterior amygdalar nucleus PA Vip-IRES-Cre 299656382 -2.54 3.00 4.55 0 Posterior complex of the thalamus PO C57BL/6J 100147785 -2.06 1.25 2.97 0 Posterior complex of the thalamus PO C57BL/6J 146658879 -2.18 1.45 2.64 0 Posterior complex of the thalamus PO C57BL/6J 174781014 -1.70 1.25 3.05 0 Posterior complex of the thalamus PO C57BL/6J 180628971 -1.94 1.60 3.40 0 Posterior complex of the thalamus PO C57BL/6J 180708524 -1.50 1.25 3.05 0 Posterior complex of the thalamus PO Grik4-Cre 183011353 -2.06 1.25 2.97 0 Posterior complex of the thalamus PO Grik4-Cre 267999740 -2.06 1.25 2.97 0 Posterior complex of the thalamus PO Grik4-Cre 292212456 -2.06 1.25 2.97 0 Posterior complex of the thalamus PO Slc17a6-IRESCre 305425490 -2.06 1.25 2.97 0 Posterior complex of the thalamus PO Slc18a2Cre_OZ14 182892855 -1.82 1.50 3.25 0 Posterior complex of the thalamus PO Slc18a2Cre_OZ14 301674988 -1.82 1.60 3.30 0 Posterior hypothalamic nucleus PH C57BL/6J 100141434 -1.34 1.00 4.89 0 Posterior hypothalamic nucleus PH C57BL/6J 114045733 -2.35 0.13 4.98 0 Posterior hypothalamic nucleus PH C57BL/6J 127710392 -1.70 0.35 5.00 0 Posterior hypothalamic nucleus PH C57BL/6J 159649643 -1.50 0.35 5.20 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 68 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Posterior hypothalamic nucleus PH C57BL/6J 175374275 0.38 0.30 2.30 0 Posterior hypothalamic nucleus PH Calb2-IRES-Cre 267213793 -2.30 0.15 4.40 0 Posterior hypothalamic nucleus PH Cart-Tg1-Cre 176898557 0.38 0.50 3.90 0 Posterior hypothalamic nucleus PH Gad2-IRES-Cre 302086846 -2.30 0.15 4.40 0 Posterior hypothalamic nucleus PH Grm2-Cre_MR90 182182936 -2.35 0.13 5.10 0 Posterior hypothalamic nucleus PH Htr2aCre_KM207 293255030 -2.70 0.13 5.20 0 Posterior hypothalamic nucleus PH Oxtr-Cre_ON66 278260569 -2.30 0.15 4.40 0 Posterior hypothalamic nucleus PH Ppp1r17Cre_NL146 268204599 -2.30 0.15 4.40 0 Posterior hypothalamic nucleus PH Ppp1r17Cre_NL146 268208632 -2.30 0.25 3.90 0 Posterior hypothalamic nucleus PH Sim1-Cre 164986046 -2.30 0.25 4.37 0 Posterior limiting nucleus of the thalamus POL Grm2-Cre_MR90 166267651 -3.16 1.60 2.89 0 Posterior limiting nucleus of the thalamus POL Pdzk1ip1Cre_KD31 170947610 -3.16 1.60 2.85 0 Posterior parietal association areas PTLp A930038C07RikTg1-Cre 168165712 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp A930038C07RikTg1-Cre 292792724 -2.46 2.75 0.35, 0.75 0 Posterior parietal association areas PTLp C57BL/6J 100148503 -2.54 1.75 0.20 0 Posterior parietal association areas PTLp C57BL/6J 112229103 -2.54 1.20 0.40 0 Posterior parietal association areas PTLp C57BL/6J 126861679 -2.54 1.75 0.55, 0.20 0 Posterior parietal association areas PTLp C57BL/6J 277714322 -3.28 2.50 0.50 0 Posterior parietal association areas PTLp Cux2-IRES-Cre 184167484 -2.54 1.75 0.20 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 69 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Posterior parietal association areas PTLp Cux2-IRES-Cre 286301303 -2.46 2.75 0.35 0 Posterior parietal association areas PTLp Cux2-IRES-Cre 294434867 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Efr3aCre_NO108 267761438 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Efr3aCre_NO108 286773358 -3.28 2.50 0.25, 0.75 0 Posterior parietal association areas PTLp Efr3aCre_NO108 309515141 -3.16 1.55 0.17 0 Posterior parietal association areas PTLp Etv1-CreERT2 182896517 -2.54 1.75 0.55, 0.20 0 Posterior parietal association areas PTLp Gpr26Cre_KO250 267657327 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Ntsr1Cre_GN220 156671933 -2.54 1.75 0.55, 0.20 0 Posterior parietal association areas PTLp Rbp4-Cre_KL100 272929308 -2.46 2.75 0.35, 0.75 0 Posterior parietal association areas PTLp Rorb-IRES2-Cre 287225041 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Scnn1a-Tg3-Cre 184073678 -2.46 3.28 0.21, 0.65 30 Posterior parietal association areas PTLp Scnn1a-Tg3-Cre 268038969 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Sim1-Cre_KJ18 293821389 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Sim1-Cre_KJ18 297712045 -2.46 2.75 0.35, 0.75 0 Posterior parietal association areas PTLp Sst-IRES-Cre 288264047 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Syt6-Cre_KI148 157769139 -2.54 1.75 0.20, 0.55 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 70 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Posterior parietal association areas PTLp Syt6-Cre_KI148 299820770 -2.46 2.75 0.35, 0.75 0 Posterior parietal association areas PTLp Tlx3-Cre_PL56 294533406 -2.54 1.75 0.20, 0.55 0 Posterior parietal association areas PTLp Tlx3-Cre_PL56 297233422 -3.16 1.55 0.17, 0.58 0 Posterior parietal association areas PTLp Tlx3-Cre_PL56 303616127 -2.46 2.75 0.35, 0.75 0 Posterior parietal association areas PTLp Trib2-2ACreERT2 287601808 -2.54 1.75 0.20, 0.55 0 Posterior pretectal nucleus PPT Pdzk1ip1Cre_KD31 264097661 -2.50 0.75 2.40 0 Posterolateral visual area VISpl C57BL/6J 272916202 -4.60 3.80 0.45 30 Posterolateral visual area VISpl Rbp4-Cre_KL100 286417464 -4.60 3.80 0.45 30 Posterolateral visual area VISpl Scnn1a-Tg3-Cre 257667118 -4.60 3.80 0.45 30 posteromedial visual area VISpm A930038C07RikTg1-Cre 286836394 -4.48 1.60 0.31 0 posteromedial visual area VISpm Nr5a1-Cre 177781745 -4.48 1.60 0.31 0 posteromedial visual area VISpm Ntsr1Cre_GN220 159554010 -4.48 1.60 0.31 0 posteromedial visual area VISpm Ntsr1Cre_GN220 297629282 -4.84 2.50 0.75 0 posteromedial visual area VISpm Oxtr-Cre_ON66 294312537 -4.84 2.50 0.31 0 posteromedial visual area VISpm Rbp4-Cre_KL100 168164230 -4.48 1.60 0.31 0 posteromedial visual area VISpm Rbp4-Cre_KL100 272930013 -4.84 2.50 0.31 0 posteromedial visual area VISpm Scnn1a-Tg3-Cre 184074388 -4.84 2.50 0.31 0 posteromedial visual area VISpm Scnn1a-Tg3-Cre 268040381 -4.48 1.60 0.31 0 posteromedial visual area VISpm Syt6-Cre_KI148 267032286 -4.84 2.50 0.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 71 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Postpiriform transition area TR C57BL/6J 126653015 -2.92 3.55 4.10 0 Postsubiculum POST C57BL/6J 126115436 -4.48 2.40 1.80 0 Postsubiculum POST C57BL/6J 127711098 -4.60 2.30 1.63 0 Postsubiculum POST Gad2-IRES-Cre 302217570 -4.16 2.25 2.27 0 Postsubiculum POST Htr2aCre_KM207 304694156 -4.04 2.00 1.50 0 Postsubiculum POST Oxtr-Cre_ON66 300623424 -4.04 2.00 1.50 0 Postsubiculum POST Scnn1a-Tg3-Cre 113934579 -4.04 2.00 1.50 0 Postsubiculum POST Scnn1a-Tg3-Cre 156314054 -4.60 2.30 1.63 0 Postsubiculum POST Slc17a6-IRESCre 167654019 -4.60 2.30 1.67 0 Prelimbic area PL A930038C07RikTg1-Cre 292374777 2.10 0.06, 0.33 1.50 0 Prelimbic area PL C57BL/6J 157711748 2.10 0.25 1.50 0 Prelimbic area PL Cux2-IRES-Cre 278433737 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Cux2-IRES-Cre 294396492 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Cux2-IRES-Cre 294434161 1.10 0.25 1.30 0 Prelimbic area PL Glt25d2Cre_NF107 305618479 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Grp-Cre_KH288 266582782 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Grp-Cre_KH288 292477301 2.68 0.05, 0.35 1.45 0 Prelimbic area PL Htr2aCre_KM207 266816894 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Ntsr1Cre_GN220 161463521 2.10 0.06, 0.33 1.50 0 Prelimbic area PL Rbp4-Cre_KL100 263106036 2.10 0.06, 0.33 1.50 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 72 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Presubiculum PRE C57BL/6J 146984915 -3.80 2.40 2.85 0 Presubiculum PRE Grm2-Cre_MR90 287172689 -3.80 2.40 2.85 0 Presubiculum PRE Rbp4-Cre_KL100 287028480 -4.72 3.40 2.20, 2.60 0 Presubiculum PRE Satb2-Cre_MO23 178488859 -4.96 3.00 2.55 0 Presubiculum PRE Scnn1a-Tg3-Cre 287772112 -4.60 2.40 2.55 0 Presubiculum PRE Slc17a6-IRESCre 302084009 -4.60 2.40 2.55 0 Primary auditory area AUDp A930038C07RikTg1-Cre 156395997 -2.46 4.25 0.81 0 Primary auditory area AUDp C57BL/6J 100149109 -2.46 4.25 0.81 0 Primary auditory area AUDp C57BL/6J 120491896 -2.54 4.20 1.25 0 Primary auditory area AUDp Calb2-IRES-Cre 168455487 -0.70 3.50 0.35, 0.75 30 Primary auditory area AUDp Chrna2Cre_OE25 296047084 -2.46 4.35 0.90 0 Primary auditory area AUDp Cort-T2A-Cre 165975810 -2.46 4.25 0.81 0 Primary auditory area AUDp Crh-IRES-Cre (BL) 183105218 -2.46 4.35 0.85 0 Primary auditory area AUDp Cux2-IRES-Cre 184159706 -2.46 4.35 0.85 0 Primary auditory area AUDp Etv1-CreERT2 156493815 -2.46 4.25 0.81 0 Primary auditory area AUDp Gad2-IRES-Cre 182934777 -2.46 4.35 0.85 0 Primary auditory area AUDp Gng7-Cre_KH71 157954927 -0.70 3.50 0.35, 0.75 30 Primary auditory area AUDp Gpr26Cre_KO250 181600380 -2.46 4.25 0.81 0 Primary auditory area AUDp Htr3aCre_NO152 305488671 -2.46 4.35 0.90 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 73 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary auditory area AUDp Nos1-CreERT2 267930268 -2.46 4.35 0.90 0 Primary auditory area AUDp Ntsr1Cre_GN220 266963362 -2.46 4.35 0.90 0 Primary auditory area AUDp Rbp4-Cre_KL100 182090318 -2.46 4.35 0.85 0 Primary auditory area AUDp Rorb-IRES2-Cre 287223629 -2.46 4.35 0.90 0 Primary auditory area AUDp Scnn1a-Tg3-Cre 166268376 -2.46 4.25 0.81 0 Primary auditory area AUDp Sim1-Cre_KJ18 293820681 -2.46 4.35 0.90 0 Primary auditory area AUDp Sst-IRES-Cre 182886547 -2.46 4.35 0.85 0 Primary auditory area AUDp Syt6-Cre_KI148 124060405 -2.46 4.25 0.81 0 Primary auditory area AUDp Trib2-2ACreERT2 182686935 -2.46 4.35 0.85 0 Primary auditory area AUDp Vip-IRES-Cre 182040934 -2.46 4.25 0.81 0 Primary motor area MOp A930038C07RikTg1-Cre 156394513 1.34 1.50 0.35, 0.75 0 Primary motor area MOp A930038C07RikTg1-Cre 287461719 0.62 1.50 0.35, 0.70 0 Primary motor area MOp A930038C07RikTg1-Cre 292374068 2.10 2.25 0.35, 1.00 30 Primary motor area MOp C57BL/6J 100141220 0.62 1.50 0.35, 0.70 0 Primary motor area MOp C57BL/6J 100141273 -0.34 1.50 0.45 0 Primary motor area MOp C57BL/6J 100141563 0.14 1.75 0.45 0 Primary motor area MOp C57BL/6J 100141780 1.10 2.00 0.30, 0.75 20 Primary motor area MOp C57BL/6J 112670853 2.10 2.25 0.35, 1.00 30 Primary motor area MOp C57BL/6J 112935169 -0.34 1.65 0.45 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 74 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary motor area MOp C57BL/6J 127084296 0.62 1.50 0.35, 0.70 0 Primary motor area MOp C57BL/6J 141602484 1.34 1.50 0.35, 0.75 0 Primary motor area MOp C57BL/6J 180709942 1.94 2.50 1.15 0 Primary motor area MOp C57BL/6J 180719293 2.10 2.40 0.40, 1.00 30 Primary motor area MOp C57BL/6J 180720175 -0.82 1.05 0.65 0 Primary motor area MOp Calb2-IRES-Cre 168454779 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Chrna2Cre_OE25 267750528 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Chrna2Cre_OE25 298273313 0.62 1.50 0.35, 0.70 0 Primary motor area MOp Chrnb4Cre_OL57 297987980 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Cort-T2A-Cre 157826227 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Crh-IRES-Cre (BL) 183103805 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Cux2-IRES-Cre 168002073 1.34 1.50 0.35 0 Primary motor area MOp Cux2-IRES-Cre 182616478 -0.54 1.65 0.45 0 Primary motor area MOp Cux2-IRES-Cre 263781454 0.14 0.90 0.40 0 Primary motor area MOp Cux2-IRES-Cre 266645328 2.10 2.25 0.35 30 Primary motor area MOp Cux2-CreERT2 310194040 1.70 1.85 2.83 0 Primary motor area MOp Efr3aCre_NO108 278258780 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Efr3aCre_NO108 288169135 0.62 1.50 0.35, 0.70 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 75 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary motor area MOp Erbb4-2ACreERT2 127908879 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Esr1-2A-Cre 264249312 -1.50 0.78 5.76 0 Primary motor area MOp Etv1-CreERT2 167569313 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Gad2-IRES-Cre 167440619 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Gpr26Cre_KO250 181598954 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Gpr26Cre_KO250 301267162 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Grp-Cre_KH288 265289624 0.26 0.27 1.25 0 Primary motor area MOp Htr2aCre_KM207 183617432 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Htr2aCre_KM207 258915564 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Htr3aCre_NO152 305487964 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Nr5a1-Cre 265929196 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Ntsr1Cre_GN220 120584036 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Ntsr1Cre_GN220 157909001 -0.34 1.65 0.45 0 Primary motor area MOp Ntsr1Cre_GN220 159372889 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Plxnd1-Cre 297669605 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Pvalb-IRES-Cre 158138440 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Rasgrf2-2A-dCre 298718072 1.34 1.50 0.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 76 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary motor area MOp Rbp4-Cre_KL100 120814821 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Rbp4-Cre_KL100 166082128 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Rbp4-Cre_KL100 166082842 -0.34 1.65 0.45 0 Primary motor area MOp Rbp4-Cre_KL100 182803137 -0.34 1.65 0.45 0 Primary motor area MOp Sim1-Cre_KJ18 287807030 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Sim1-Cre_KJ18 287807743 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Sim1-Cre_KJ18 297711339 0.62 1.50 0.35, 0.70 0 Primary motor area MOp Sim1-Cre_KJ18 297946935 2.10 2.25 0.35, 1.00 30 Primary motor area MOp Sst-IRES-Cre 277800995 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Syt6-Cre_KI148 122642490 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Syt6-Cre_KI148 168229113 0.62 1.50 0.35, 0.70 0 Primary motor area MOp Tac1-IRES2-Cre 181259279 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Tlx3-Cre_PL56 288169842 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Trib2-2ACreERT2 266176167 1.34 1.50 0.35, 0.75 0 Primary motor area MOp Vip-IRES-Cre 179904912 1.34 1.50 0.35, 0.75 0 Primary somatosensory area SSp Nr5a1-Cre 277851379 -2.46 3.28 0.21, 0.65 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 77 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area SSp Nr5a1-Cre 293548317 -2.46 2.75 0.35, 0.75 0 Primary somatosensory area, barrel field SSp-bfd A930038C07RikTg1-Cre 171276330 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd A930038C07RikTg1-Cre 177907797 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd A930038C07RikTg1-Cre 182467026 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd A930038C07RikTg1-Cre 298326521 -0.22 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 100141473 -2.54 3.50 0.45 30 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 112162251 -0.58 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 112373124 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 112882565 -2.46 3.75 0.65 0 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 112951804 -1.70 3.88, 3.38 1.25 0 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 126908007 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 127866392 -1.70 4.00 0.65 0 Primary somatosensory area, barrel field SSp-bfd Calb2-IRES-Cre 168513750 -2.46 4.25 0.81 0 Primary somatosensory area, barrel field SSp-bfd Cart-Tg1-Cre 159602992 -1.46 3.55 3.70 0 Primary somatosensory area, barrel field SSp-bfd Chrna2Cre_OE25 267749821 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Chrna2Cre_OE25 293889922 -1.82 3.20 0.35, 0.75 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 78 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, barrel field SSp-bfd Cort-T2A-Cre 167374643 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Crh-IRES-Cre (BL) 266913240 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Cux2-IRES-Cre 168003640 -0.70 3.50 0.35 30 Primary somatosensory area, barrel field SSp-bfd Cux2-IRES-Cre 266486371 -1.82 3.20 0.35 30 Primary somatosensory area, barrel field SSp-bfd Drd3-Cre_KI196 293728197 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Drd3-Cre_KI196 297671018 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Drd3-Cre_KI196 309427991 0.26 3.50 0.35 30 Primary somatosensory area, barrel field SSp-bfd Drd3-Cre_KI196 309514434 -0.70 3.50 1.70 0 Primary somatosensory area, barrel field SSp-bfd Efr3aCre_NO108 267660272 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Efr3aCre_NO108 286648997 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Efr3aCre_NO108 292318449 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Erbb4-2ACreERT2 127993375 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Etv1-CreERT2 286772650 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Gad2-IRES-Cre 167441329 -0.70 3.50 0.35, 0.75 0 Primary somatosensory area, barrel field SSp-bfd Gng7-Cre_KH71 158017916 -4.48 2.70 0.35 0 Primary somatosensory area, barrel field SSp-bfd Gpr26Cre_KO250 175819113 -1.82 3.00 0.35, 0.75 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 79 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, barrel field SSp-bfd Gpr26Cre_KO250 181599674 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Htr3aCre_NO152 305487234 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Nos1-CreERT2 182043055 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Nr5a1-Cre 176881134 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Nr5a1-Cre 177322838 -0.70 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 159321097 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 159651770 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 181180790 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 287037604 -0.34 3.50 2.95 0 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 297628576 -2.46 2.75 0.35, 0.75 0 Primary somatosensory area, barrel field SSp-bfd Ntsr1Cre_GN220 303617548 -0.22 3.38, 3.88 1.66 0 Primary somatosensory area, barrel field SSp-bfd Penk-IRES2-Cre 306268688 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Plxnd1-Cre 297668898 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Pvalb-IRES-Cre 158139151 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Pvalb-IRES-Cre 176496282 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Rasgrf2-2A-dCre 298718778 -0.70 3.50 0.35 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 80 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 120875816 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 120916102 -2.46 4.25 0.81 0 Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 249327301 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 272735030 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 298179622 -2.46 4.25 0.81 0 Primary somatosensory area, barrel field SSp-bfd Rbp4-Cre_KL100 303785454 0.26 3.50 0.35 30 Primary somatosensory area, barrel field SSp-bfd Rorb-IRES2-Cre 287174103 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Rorb-IRES2-Cre 301583889 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Scnn1a-Tg3-Cre 159888336 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Scnn1a-Tg3-Cre 181818339 -0.70 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd Scnn1a-Tg3-Cre 181819064 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Scnn1a-Tg3-Cre 183374804 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Scnn1a-Tg3-Cre 257666283 -0.22 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd Sim1-Cre_KJ18 297710633 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Sim1-Cre_KJ18 297713365 -0.70 4.00, 3.50 1.70 0 Primary somatosensory area, barrel field SSp-bfd Sim1-Cre_KJ18 297948420 0.26 3.50 0.35, 0.75 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 81 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, barrel field SSp-bfd Sim1-Cre_KJ18 297985755 -0.22 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd Sim1-Cre_KJ18 298760261 -0.70 3.50 0.35, 0.75 0 Primary somatosensory area, barrel field SSp-bfd Slc18a2Cre_OZ14 263370720 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Slc18a2Cre_OZ14 265820951 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Slc18a2Cre_OZ14 306959448 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Sst-IRES-Cre 277801701 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Syt6-Cre_KI148 123664417 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Syt6-Cre_KI148 159223769 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Syt6-Cre_KI148 168096467 -0.70 3.88, 3.38 1.66 0 Primary somatosensory area, barrel field SSp-bfd Syt6-Cre_KI148 168229820 0.26 3.50 0.35, 0.75 0 Primary somatosensory area, barrel field SSp-bfd Syt6-Cre_KI148 178487444 -2.46 3.28 0.21, 0.65 30 Primary somatosensory area, barrel field SSp-bfd Tac1-IRES2-Cre 181371331 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Tlx3-Cre_PL56 288170549 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Tlx3-Cre_PL56 288171256 -2.46 4.35 0.90 0 Primary somatosensory area, barrel field SSp-bfd Trib2-2ACreERT2 266172624 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, barrel field SSp-bfd Vip-IRES-Cre 180075597 -0.70 3.50 0.35, 0.75 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 82 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, lower limb SSp-ll A930038C07RikTg1-Cre 166323186 -1.06 2.25 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll A930038C07RikTg1-Cre 166461193 -0.34 1.65 0.45 0 Primary somatosensory area, lower limb SSp-ll A930038C07RikTg1-Cre 264629246 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, lower limb SSp-ll A930038C07RikTg1-Cre 281459203 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll C57BL/6J 112229814 -0.58 2.25 0.35, 0.75 20 Primary somatosensory area, lower limb SSp-ll C57BL/6J 114292355 -0.82 1.40 0.45 0 Primary somatosensory area, lower limb SSp-ll C57BL/6J 126852363 -1.58 1.50 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll C57BL/6J 148964212 -0.30 2.00 4.85 0 Primary somatosensory area, lower limb SSp-ll C57BL/6J 180718587 -0.58 1.90 0.70 0 Primary somatosensory area, lower limb SSp-ll Chrna2Cre_OE25 292124765 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll Chrna2Cre_OE25 292173552 -0.34 2.10 0.45 0 Primary somatosensory area, lower limb SSp-ll Cux2-IRES-Cre 266644610 -0.34 1.85 0.45 0 Primary somatosensory area, lower limb SSp-ll Cux2-IRES-Cre 286300594 0.38 2.50 0.40 15 Primary somatosensory area, lower limb SSp-ll Efr3aCre_NO108 278257366 -0.34 2.10 0.45 0 Primary somatosensory area, lower limb SSp-ll Gpr26Cre_KO250 267658747 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, lower limb SSp-ll Htr2aCre_KM207 277957908 0.62 1.50 0.35, 0.70 0 Primary somatosensory area, lower limb SSp-ll Nr5a1-Cre 166566678 -1.06 2.25 0.35, 0.75 25 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 83 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, lower limb SSp-ll Ntsr1Cre_GN220 266964788 -0.34 1.90 0.45 0 Primary somatosensory area, lower limb SSp-ll Rasgrf2-2A-dCre 303713313 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll Rbp4-Cre_KL100 272698650 -0.34 2.00 0.45 0 Primary somatosensory area, lower limb SSp-ll Rorb-IRES2-Cre 287880102 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, lower limb SSp-ll Rorb-IRES2-Cre 293700454 -0.34 2.10 0.45 0 Primary somatosensory area, lower limb SSp-ll Scnn1a-Tg3-Cre 166326029 -1.06 2.25 0.35, 0.75 25 Primary somatosensory area, lower limb SSp-ll Scnn1a-Tg3-Cre 179640955 -0.34 1.65 0.45 0 Primary somatosensory area, lower limb SSp-ll Sim1-Cre_KJ18 297714071 -0.34 2.10 0.45 0 Primary somatosensory area, lower limb SSp-ll Slc18a2Cre_OZ14 266643194 -0.34 1.85 0.45 0 Primary somatosensory area, lower limb SSp-ll Syt6-Cre_KI148 156786234 -0.34 1.65 0.45 0 Primary somatosensory area, lower limb SSp-ll Tlx3-Cre_PL56 296052839 -0.34 2.10 0.45 0 Primary somatosensory area, lower limb SSp-ll Trib2-2ACreERT2 292620251 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, mouth SSp-m A930038C07RikTg1-Cre 298796577 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, mouth SSp-m C57BL/6J 112936582 0.74 3.25 0.35, 0.75 0 Primary somatosensory area, mouth SSp-m C57BL/6J 114290938 0.74 3.70 0.40, 0.80 60 Primary somatosensory area, mouth SSp-m C57BL/6J 157654817 1.10 3.30 1.15 0 Primary somatosensory area, mouth SSp-m Cux2-IRES-Cre 278317945 0.26 3.50 0.35 30 Primary somatosensory area, mouth SSp-m Cux2-IRES-Cre 294397199 1.10 3.25, 3.00 1.90, 2.35 0 Primary somatosensory area, mouth SSp-m Nr5a1-Cre 177782493 0.26 3.50 0.35, 0.75 30 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 84 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, mouth SSp-m Rorb-IRES2-Cre 301581763 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, mouth SSp-m Scnn1a-Tg3-Cre 277852088 1.10 3.25, 3.00 1.90, 2.35 0 Primary somatosensory area, trunk SSp-tr C57BL/6J 100141495 -1.06 1.50 0.45 0 Primary somatosensory area, trunk SSp-tr C57BL/6J 100142655 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr C57BL/6J 112791318 -1.06 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr C57BL/6J 126907302 -2.46 3.28 0.21, 0.65 30 Primary somatosensory area, trunk SSp-tr Chrna2Cre_OE25 278175580 -2.54 1.75 0.20, 0.55 0 Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 178284661 -1.06 2.25 0.35 25 Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 294435580 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr Cux2-IRES-Cre 298830161 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr Efr3aCre_NO108 277907462 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr Gpr26Cre_KO250 298404154 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, trunk SSp-tr Nr5a1-Cre 115956702 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr Ntsr1Cre_GN220 157768393 -1.06 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr Ntsr1Cre_GN220 166533924 -2.46 3.28 0.21, 0.65 30 Primary somatosensory area, trunk SSp-tr Ntsr1Cre_GN220 304641170 -1.34 1.50 0.35, 0.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 85 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, trunk SSp-tr Rbp4-Cre_KL100 183171679 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr Rbp4-Cre_KL100 297652799 -1.06 2.25 0.35 25 Primary somatosensory area, trunk SSp-tr Scnn1a-Tg3-Cre 166459070 -1.82 3.00 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr Sim1-Cre_KJ18 299784429 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, trunk SSp-tr Slc18a2Cre_OZ14 263553163 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr Sst-IRES-Cre 304335875 -1.82 2.65 4.25 0 Primary somatosensory area, trunk SSp-tr Syt6-Cre_KI148 177319236 -1.06 2.25 0.35, 0.75 25 Primary somatosensory area, trunk SSp-tr Tlx3-Cre_PL56 297654263 -1.82 3.20 0.35, 0.75 30 Primary somatosensory area, trunk SSp-tr Tlx3-Cre_PL56 298182842 -1.34 1.50 0.35, 0.75 0 Primary somatosensory area, unassigned SSp-un C57BL/6J 272697944 1.90 2.40 1.25 0 Primary somatosensory area, unassigned SSp-un Scnn1a-Tg3-Cre 299447873 1.10 3.25, 3.0 1.90, 2.35 0 Primary somatosensory area, upper limb SSp-ul A930038C07RikTg1-Cre 292792016 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul C57BL/6J 126909424 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Chrna2Cre_OE25 298325807 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Cux2-IRES-Cre 298106713 0.38 2.50 0.40 15 Primary somatosensory area, upper limb SSp-ul Drd3-Cre_KI196 309428697 0.38 2.50 0.40 15 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 86 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary somatosensory area, upper limb SSp-ul Efr3aCre_NO108 298352336 0.38 2.50 0.4, 0.75 15 Primary somatosensory area, upper limb SSp-ul Etv1-CreERT2 167570021 -0.70 3.50 0.35, 0.75 30 Primary somatosensory area, upper limb SSp-ul Nr5a1-Cre 177893658 0.35 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Ntsr1Cre_GN220 159651060 0.62 1.50 0.35, 0.70 0 Primary somatosensory area, upper limb SSp-ul Ntsr1Cre_GN220 162017460 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Rbp4-Cre_KL100 266249483 -1.34 2.25 0.35, 0.75 25 Primary somatosensory area, upper limb SSp-ul Rbp4-Cre_KL100 286312782 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Scnn1a-Tg3-Cre 181860173 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Sim1-Cre_KJ18 297951732 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Slc18a2Cre_OZ14 306990880 0.38 2.50 0.4, 0.75 15 Primary somatosensory area, upper limb SSp-ul Syt6-Cre_KI148 179641666 0.38 2.50 0.40, 0.75 15 Primary somatosensory area, upper limb SSp-ul Tlx3-Cre_PL56 303614706 0.26 3.50 0.35, 0.75 30 Primary somatosensory area, upper limb SSp-ul Tlx3-Cre_PL56 303615412 0.38 2.50 0.4, 0.75 15 Primary visual area VISp A930038C07RikTg1-Cre 158255941 -4.48 2.70 0.35 0 Primary visual area VISp A930038C07RikTg1-Cre 166324604 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp A930038C07RikTg1-Cre 283020912 -3.28 2.50 0.25, 0.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 87 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary visual area VISp A930038C07RikTg1-Cre 292793967 -4.84 2.50 0.31 0 Primary visual area VISp A930038C07RikTg1-Cre 298351630 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp C57BL/6J 100141219 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp C57BL/6J 100147853 -4.48 2.70 0.35 0 Primary visual area VISp C57BL/6J 113887162 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp C57BL/6J 113887868 -4.84 2.50 0.31 0 Primary visual area VISp C57BL/6J 126862385 -4.48 1.60 0.31 0 Primary visual area VISp C57BL/6J 127138787 -4.60 3.60 0.45 30 Primary visual area VISp C57BL/6J 174361040 -4.36 1.65 0.38 0 Primary visual area VISp C57BL/6J 180296424 -4.60 3.45 0.80 0 Primary visual area VISp C57BL/6J 272782668 -4.48 1.62 0.31 0 Primary visual area VISp C57BL/6J 277616630 -3.28 2.50 0.50 0 Primary visual area VISp C57BL/6J 277712166 -3.28 2.50 0.50 0 Primary visual area VISp C57BL/6J 277713580 -3.28 2.50 0.50 0 Primary visual area VISp Calb2-IRES-Cre 168515938 -4.48 2.70 0.35 0 Primary visual area VISp Chrna2Cre_OE25 278068196 -2.46 4.35 0.90 0 Primary visual area VISp Chrna2Cre_OE25 292126180 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Chrna2Cre_OE25 297597186 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Chrna2Cre_OE25 299781566 -4.84 2.50 0.31 0 Primary visual area VISp Cort-T2A-Cre 167375352 -4.48 2.70 0.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 88 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary visual area VISp Crh-IRES-Cre (BL) 266836749 -4.48 2.70 0.35 0 Primary visual area VISp Cux2-IRES-Cre 183471884 -4.48 2.70 0.35 0 Primary visual area VISp Cux2-IRES-Cre 272821309 -3.28 2.50 0.25 0 Primary visual area VISp Cux2-IRES-Cre 286302294 -4.84 2.50 0.31 0 Primary visual area VISp Cux2-IRES-Cre 293472335 -3.28 2.50 0.25 0 Primary visual area VISp Cux2-IRES-Cre 298829455 -4.60 3.80 0.45 30 Primary visual area VISp Drd3-Cre_KI196 298759552 -4.84 2.50 0.75 0 Primary visual area VISp Efr3aCre_NO108 267704653 -4.48 2.70 0.35 0 Primary visual area VISp Efr3aCre_NO108 286835688 -3.40 3.60 0.45 0 Primary visual area VISp Efr3aCre_NO108 298350212 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Efr3aCre_NO108 294266031 -4.60 3.80 0.45 30 Primary visual area VISp Efr3aCre_NO108 309564818 -4.04 4.00 0.35 0 Primary visual area VISp Erbb4-2ACreERT2 182184486 -4.48 2.70 0.35 0 Primary visual area VISp Etv1-CreERT2 156494530 -4.48 2.70 0.35 0 Primary visual area VISp Gad2-IRES-Cre 167511639 -4.48 2.70 0.35 0 Primary visual area VISp Gng7-Cre_KH71 157955639 -2.46 4.25 0.81 0 Primary visual area VISp Gpr26Cre_KO250 181601101 -4.48 2.70 0.35 0 Primary visual area VISp Gpr26Cre_KO250 301263519 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Htr3aCre_NO152 305489377 -4.48 2.70 0.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 89 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary visual area VISp Nos1-CreERT2 267931685 -4.48 2.70 0.35 0 Primary visual area VISp Nos1-CreERT2 293116943 -4.48 2.70 0.35 0 Primary visual area VISp Nr5a1-Cre 176882966 -3.40 3.50 0.45 0 Primary visual area VISp Nr5a1-Cre 176901480 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Nr5a1-Cre 177781006 -3.80 2.00 0.35, 0.75 0 Primary visual area VISp Nr5a1-Cre 266100645 -4.84 2.50 0.31 0 Primary visual area VISp Nr5a1-Cre 266177248 -4.04 4.00 0.35, 0.75 30 Primary visual area VISp Ntsr1Cre_GN220 156545918 -4.48 2.70 0.35 0 Primary visual area VISp Ntsr1Cre_GN220 159550125 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Ntsr1Cre_GN220 181258571 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Ntsr1Cre_GN220 297629988 -4.60 3.80 0.45 30 Primary visual area VISp Plxnd1-Cre 299859225 -4.48 2.70 0.35 0 Primary visual area VISp Pvalb-IRES-Cre 166562678 -4.48 2.70 0.35 0 Primary visual area VISp Rasgrf2-2A-dCre 298758133 -4.48 2.70 0.35 0 Primary visual area VISp Rbp4-Cre_KL100 121510421 -4.48 2.70 0.35 0 Primary visual area VISp Rbp4-Cre_KL100 183173527 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Rbp4-Cre_KL100 266250195 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Rbp4-Cre_KL100 294482052 -3.80 2.50 0.35 0 Primary visual area VISp Rorb-IRES2-Cre 287224335 -4.48 2.70 0.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 90 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary visual area VISp Rorb-IRES2-Cre 300929973 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Rorb-IRES2-Cre 301616660 -4.48 2.70 0.35 0 Primary visual area VISp Rorb-IRES2-Cre 301617370 -4.60 3.80 0.45 30 Primary visual area VISp Scnn1a-Tg3-Cre 166269819 -4.48 2.70 0.35 0 Primary visual area VISp Scnn1a-Tg3-Cre 166326736 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Scnn1a-Tg3-Cre 182089608 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Sst-IRES-Cre 288261928 -4.48 2.70 0.35 0 Primary visual area VISp Syt6-Cre_KI148 125435783 -4.48 2.70 0.35 0 Primary visual area VISp Syt6-Cre_KI148 156784823 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Syt6-Cre_KI148 159330030 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Syt6-Cre_KI148 168097187 -4.48 1.60 0.31 0 Primary visual area VISp Syt6-Cre_KI148 297671724 -4.84 2.50 0.75 0 Primary visual area VISp Syt6-Cre_KI148 299828473 -4.60 3.80 0.45 30 Primary visual area VISp Tlx3-Cre_PL56 288171964 -4.48 2.70 0.35 0 Primary visual area VISp Tlx3-Cre_PL56 296052133 -3.80 2.50 0.35, 0.75 0 Primary visual area VISp Tlx3-Cre_PL56 297592527 -3.28 2.50 0.25, 0.75 0 Primary visual area VISp Tlx3-Cre_PL56 297593235 -4.84 2.50 0.31 0 Primary visual area VISp Tlx3-Cre_PL56 297593942 -4.60 3.80 0.45 30 Primary visual area VISp Trib2-2ACreERT2 268320515 -4.48 2.70 0.35 0 Primary visual area VISp Trib2-2ACreERT2 308879859 -3.80 2.50 0.35, 0.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 91 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Primary visual area VISp Vip-IRES-Cre 182293273 -4.48 2.70 0.35 0 Primary visual area, layer 4 VISp4 Nr5a1-Cre 157767683 -4.48 2.70 0.35 0 Principal sensory nucleus of the trigeminal PSV C57BL/6J 114755811 -5.20 1.95 3.35 0 Principal sensory nucleus of the trigeminal PSV C57BL/6J 156979988 -4.04 2.25 4.65 0 Principal sensory nucleus of the trigeminal PSV Gad2-IRES-Cre 303535867 -4.36 1.60 4.27 0 Principal sensory nucleus of the trigeminal PSV Syt6-Cre_KI148 182465608 -4.36 1.60 4.27 0 Pyramus (VIII) PYR C57BL/6J 125831616 -7.32 0.50 1.63 0 Red nucleus RN C57BL/6J 113400134 -3.28 0.36 4.13 0 Red nucleus RN C57BL/6J 120811946 -3.08 1.25 4.15 0 Red Nucleus RN Rbp4-Cre_KL100 300624130 -3.28 0.60 3.65 0 Reticular nucleus of the thalamus RT C57BL/6J 117316260 -0.34 1.70 3.58 0 Reticular nucleus of the thalamus RT C57BL/6J 127468854 -0.70 1.80 3.95 0 Reticular nucleus of the thalamus RT Gad2-IRES-Cre 156252954 -0.70 1.53 3.48 0 Reticular nucleus of the thalamus RT Gad2-IRES-Cre 156254369 -1.22 2.00 3.09 0 Reticular nucleus of the thalamus RT Oxtr-Cre_ON66 301421253 -2.30 2.55 3.00 0 Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 127085005 -0.70 1.53 3.48 0 Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 127090378 -1.22 2.00 3.09 0 Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 277958616 -0.70 1.80 3.95 0 Reticular nucleus of the thalamus RT Pvalb-IRES-Cre 299894738 -0.34 1.70 3.58 0 Reticular nucleus of the thalamus RT Slc32a1-IRESCre 171064488 -0.70 1.53 3.48 0 Reticular nucleus of the thalamus RT Slc32a1-IRESCre 171065200 -1.22 2.00 3.09 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 92 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Retrochiasmatic area RCH Lypd6Cre_KL156 305092904 -0.34 0.20 5.60 0 Retrosplenial area RSP A930038C07RikTg1-Cre 166271142 -2.06 0.17 0.63 0 Retrosplenial area RSP C57BL/6J 100148142 -2.06 0.17 0.63 0 Retrosplenial area RSP Chrna2Cre_OE25 298275548 -3.28 1.06 1.17 0 Retrosplenial area RSP Cux2-IRES-Cre 272735744 -3.00 0.45 0.40 0 Retrosplenial area RSP Etv1-CreERT2 159097209 -2.06 0.17 0.63 0 Retrosplenial area RSP Scnn1a-Tg3-Cre 166269090 -2.06 0.17 0.63 0 Retrosplenial area, dorsal part RSPd A930038C07RikTg1-Cre 166325321 -3.00 0.45 0.40 0 Retrosplenial area, dorsal part RSPd Adcyap1-2A-Cre 306491185 -1.70 0.42 2.45 0 Retrosplenial area, dorsal part RSPd C57BL/6J 112424813 -3.00 0.45 0.40 0 Retrosplenial area, dorsal part RSPd Chrnb4Cre_OL57 298000880 -1.70 0.42 2.45 0 Retrosplenial area, dorsal part RSPd Efr3aCre_NO108 267661018 -2.06 0.17 0.63 0 Retrosplenial area, dorsal part RSPd Efr3aCre_NO108 278179794 -3.80 2.50 0.35, 0.75 0 Retrosplenial area, dorsal part RSPd Gpr26Cre_KO250 267658040 -2.06 0.17 0.63 0 Retrosplenial area, dorsal part RSPd Gpr26Cre_KO250 298404860 -3.80 2.50 0.35, 0.75 0 Retrosplenial area, dorsal part RSPd Gpr26Cre_KO250 298720191 -3.00 0.45 0.40 0 Retrosplenial area, dorsal part RSPd Rbp4-Cre_KL100 166054929 -3.00 0.45 0.40 0 Retrosplenial area, dorsal part RSPd Scnn1a-Tg3-Cre 166458363 -3.00 0.45 0.40 0 Retrosplenial area, dorsal part RSPd Sst-IRES-Cre 288264753 -2.06 0.17 0.63 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 93 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Retrosplenial area, lateral agranular part RSPagl C57BL/6J 272916915 -3.16 1.20 0.55 0 Retrosplenial area, lateral agranular part RSPagl Chrna2Cre_OE25 297627858 -4.48 1.60 0.31 0 Retrosplenial area, lateral agranular part RSPagl Cux2-IRES-Cre 294484177 -4.48 1.60 0.31 0 Retrosplenial area, lateral agranular part RSPagl Efr3aCre_NO108 288168426 -4.48 1.60 0.31 0 Retrosplenial area, ventral part RSPv A930038C07RikTg1-Cre 292373346 -3.28 1.06 1.17 0 Retrosplenial area, ventral part RSPv C57BL/6J 100140949 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv C57BL/6J 100142354 -4.04 2.00 1.50 0 Retrosplenial area, ventral part RSPv C57BL/6J 112516334 -2.06 0.17 0.60 0 Retrosplenial area, ventral part RSPv C57BL/6J 112595376 -3.28 1.06 1.17 0 Retrosplenial area, ventral part RSPv Chrna2Cre_OE25 292124058 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Chrna2Cre_OE25 292172100 -3.00 0.45 0.40 0 Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 177907082 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 182467736 -3.00 0.45 0.40 0 Retrosplenial area, ventral part RSPv Cux2-IRES-Cre 184168193 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Drd3-Cre_KI196 304693450 -4.04 2.00 1.50 0 Retrosplenial area, ventral part RSPv Nos1-CreERT2 308027576 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 159832064 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 249396394 -3.28 1.06 1.17 0 Retrosplenial area, ventral part RSPv Rbp4-Cre_KL100 303784745 -3.28 1.06 1.17 0 Retrosplenial area, ventral part RSPv Scnn1a-Tg3-Cre 181860879 -3.28 1.06 1.17 0 Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 157711043 -3.00 0.45 0.40 0 Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 168363168 -3.28 1.06 1.17 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 94 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Retrosplenial area, ventral part RSPv Syt6-Cre_KI148 176497015 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Trib2-2ACreERT2 287601100 -2.06 0.17 0.63 0 Retrosplenial area, ventral part RSPv Trib2-2ACreERT2 308721884 -2.06 0.17 0.63 0 Secondary motor area MOs A930038C07RikTg1-Cre 166460484 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs A930038C07RikTg1-Cre 176433237 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs A930038C07RikTg1-Cre 292476595 3.70 1.50 0.40 0 Secondary motor area MOs C57BL/6J 100140756 3.08 1.50 0.40 0 Secondary motor area MOs C57BL/6J 100141454 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs C57BL/6J 112952510 1.70 0.90 0.40, 0.80 0 Secondary motor area MOs C57BL/6J 141603190 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs C57BL/6J 157710335 3.08 1.50 0.40 0 Secondary motor area MOs C57BL/6J 180916954 0.14 0.60 0.60 0 Secondary motor area MOs Chrna2Cre_OE25 292172846 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Chrna2Cre_OE25 292174974 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Chrna2Cre_OE25 292210312 2.10 2.25 0.35, 1.00 30 Secondary motor area MOs Chrnb4Cre_OL57 298000163 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Crh-IRES-Cre (BL) 183172820 0.26 0.27 0.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 95 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Secondary motor area MOs Cux2-IRES-Cre 182461051 2.10 0.75 0.35 0 Secondary motor area MOs Cux2-IRES-Cre 272822110 1.00 0.75 0.30 0 Secondary motor area MOs Cux2-IRES-Cre 286299886 3.70 1.50 0.40 0 Secondary motor area MOs Efr3aCre_NO108 267659565 1.34 1.50 0.35, 0.75 0 Secondary motor area MOs Efr3aCre_NO108 278181912 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Efr3aCre_NO108 278258073 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Efr3aCre_NO108 287995889 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Etv1-CreERT2 156492394 1.34 1.50 0.35, 0.75 0 Secondary motor area MOs Glt25d2Cre_NF107 313327735 2.80 1.25 1.30 0 Secondary motor area MOs Gpr26Cre_KO250 258316155 0.26 0.27 0.60 0 Secondary motor area MOs Gpr26Cre_KO250 298601161 2.10 0.80 0.35, 0.75 0 Secondary motor area MOs Grm2-Cre_MR90 182795499 3.08 1.50 0.40 0 Secondary motor area MOs Grm2-Cre_MR90 182814071 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Grm2-Cre_MR90 300235349 3.10 1.50 0.40 0 Secondary motor area MOs Grp-Cre_KH288 265292679 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Grp-Cre_KH288 266503540 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Grp-Cre_KH288 292034715 2.95 1.50 0.40 0 Secondary motor area MOs Htr2aCre_KM207 277957202 1.00 0.75 0.30, 0.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 96 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Secondary motor area MOs Htr2aCre_KM207 293433996 3.70 1.50 0.40 0 Secondary motor area MOs Nos1-CreERT2 267813224 1.34 1.50 0.35, 0.75 0 Secondary motor area MOs Nos1-CreERT2 267930978 0.26 0.27 0.60 0 Secondary motor area MOs Nr5a1-Cre 167791990 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Ntsr1Cre_GN220 158139883 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Ntsr1Cre_GN220 159373612 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Ntsr1Cre_GN220 159551564 -0.34 4.00, 3.75 3.00, 3.25 0 Secondary motor area MOs Rasgrf2-2A-dCre 298758841 0.26 0.27 0.60 0 Secondary motor area MOs Rbp4-Cre_KL100 166055636 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Rbp4-Cre_KL100 168162771 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Rbp4-Cre_KL100 182793477 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Rbp4-Cre_KL100 263242463 3.08 1.50 0.40 0 Secondary motor area MOs Sim1-Cre_KJ18 293827470 2.10 0.80 0.35, 0.75 0 Secondary motor area MOs Sim1-Cre_KJ18 297854981 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Sim1-Cre_KJ18 297947641 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Syt6-Cre_KI148 159330754 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Syt6-Cre_KI148 177319974 0.14 0.90 0.40, 0.80 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 97 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Secondary motor area MOs Syt6-Cre_KI148 177459319 2.10 0.75 0.35, 0.75 0 Secondary motor area MOs Syt6-Cre_KI148 177890246 3.08 1.50 0.40 0 Secondary motor area MOs Syt6-Cre_KI148 287633753 2.10 2.25 0.35, 1.00 30 Secondary motor area MOs Tlx3-Cre_PL56 293431869 0.26 0.27 0.60 0 Secondary motor area MOs Tlx3-Cre_PL56 293432575 0.26 0.25 1.25 0 Secondary motor area MOs Tlx3-Cre_PL56 294525944 0.14 0.90 0.40, 0.80 0 Secondary motor area MOs Tlx3-Cre_PL56 294532700 2.10 0.80 0.35, 0.75 0 Secondary motor area MOs Tlx3-Cre_PL56 297892130 1.00 0.75 0.30, 0.75 0 Secondary motor area MOs Vip-IRES-Cre 182935487 0.26 0.27 0.80 0 Septofimbrial nucleus SF Calb2-IRES-Cre 287950390 -0.10 0.10 2.30 0 Septofimbrial nucleus SF Syt6-Cre_KI148 182341627 0.02 0.40 3.08 0 Simple lobule SIM C57BL/6J 112460257 -5.88 2.25 2.19 0 Simple lobule SIM C57BL/6J 113936696 -5.68 2.25 0.42, 1.05 0 Simple lobule SIM Gabra6-IRESCre 159945113 -6.48 2.50 0.57 0 Simple lobule SIM Gad2-IRES-Cre 287539649 -5.88 2.25 2.19 0 Simple lobule SIM Gad2-IRES-Cre 302079862 -4.60 2.40 2.55 0 Simple lobule SIM Nos1-CreERT2 300622004 -5.68 2.25 0.42, 1.05 0 Simple lobule SIM Pcp2Cre_GN135 168299316 -5.68 2.25 0.42, 1.05 0 Simple lobule SIM Ppp1r17Cre_NL146 267811103 -6.48 2.50 0.57 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 98 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Simple lobule SIM Ppp1r17Cre_NL146 268165349 -5.68 2.25 0.42, 1.05 0 Simple lobule SIM Slc17a7-IRES2Cre 267106046 -5.68 2.25 0.42, 1.05 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 114402050 0.20 calamus (-7.00 bregma) 1.25 0.15 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 122640358 -0.32 calamus (-7.64 bregma) 0.80 0.28 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 126352744 -6.96 1.80 3.40 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 146856593 0.30 calamus (-6.90 bregma) 1.20 0.15 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 147215105 -0.44 calamus (-7.76 bregma) 1.75 0.61 0 Spinal nucleus of the trigeminal, caudal part SPVC C57BL/6J 147790181 0.00 calamus (-7.32 bregma) 1.00 1.36 0 Spinal nucleus of the trigeminal, caudal part SPVC Cck-IRES-Cre 287460307 -0.44 calamus (-7.76 Bregma) 1.75 0.61 0 Spinal nucleus of the trigeminal, caudal part SPVC Slc32a1-IRESCre 305319461 -0.44 calamus (-7.76 Bregma) 1.75 0.61 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 99 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Spinal nucleus of the trigeminal, caudal part SPVC Slc6a5Cre_KF109 126908712 -7.56 1.25 3.06 0 Spinal nucleus of the trigeminal, caudal part SPVC Syt6-Cre_KI148 264096244 -0.44 calamus (-7.76 bregma) 1.75 0.61 0 Spinal nucleus of the trigeminal, caudal part SPVC Th-Cre 311846681 -0.44 1.75 0.61 0 Spinal nucleus of the trigeminal, interpolar part SPVI C57BL/6J 272738620 -6.84 1.80 3.40 0 Spinal nucleus of the trigeminal, interpolar part SPVI Slc6a5Cre_KF109 160150861 -6.00 1.83 3.95 0 Spinal nucleus of the trigeminal, interpolar part SPVI Slc6a5Cre_KF109 160151570 -6.96 1.80 3.40 0 Spinal nucleus of the trigeminal, oral part SPVO C57BL/6J 112826458 -6.00 1.83 3.95 0 Spinal vestibular nucleus SPIV C57BL/6J 126351299 -6.00 1.40 3.20 0 Spinal vestibular nucleus SPIV C57BL/6J 128056535 -6.48 1.25 3.25 0 Spinal vestibular nucleus SPIV C57BL/6J 129567943 -5.68 1.13 3.00 0 Striatum dorsal region CP Chat-IRES-Cre 307692311 -1.34 2.80 1.84 0 Striatum dorsal region CP Chat-IRES-Cre 307909888 -0.70 2.70 2.39 0 Striatum dorsal region CP Chat-IRES-Cre 307910595 0.14 1.75 2.53 0 Striatum dorsal region CP Efr3aCre_NO108 301180385 -1.34 2.80 1.84 0 Striatum dorsal region CP Gad2-IRES-Cre 303478748 -1.06 3.00 3.90 0 Striatum dorsal region CP Ntrk1-IRES-Cre 308395312 0.14 1.75 2.53 0 Striatum dorsal region CP Slc18a2Cre_OZ14 301620241 0.14 1.75 2.53 0 Subiculum SUB C57BL/6J 114008926 -3.52 2.50 1.35 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 100 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Subiculum, dorsal part SUBd C57BL/6J 127795906 -3.52 2.50 1.35 0 Subiculum, dorsal part SUBd C57BL/6J 157063781 -2.55 0.13 5.30 0 Subiculum, dorsal part SUBd Drd1a-Cre 113368898 -2.85 0.70 1.85 0 Subiculum, dorsal part SUBd Slc17a6-IRESCre 159374329 -4.04 2.00 1.50 0 Subiculum, dorsal part SUBd Slc32a1-IRESCre 264077561 -2.70 0.56 1.92 0 Subiculum, dorsal part SUBd Syt17-Cre_NO14 293009970 -2.92 1.85 1.95 0 Subiculum, ventral part SUBv A930038C07RikTg1-Cre 298831574 -4.72 3.40 2.2, 2.6 0 Subiculum, ventral part SUBv C57BL/6J 122641784 -2.54 4.25 3.32 25 Subiculum, ventral part SUBv C57BL/6J 127222723 -4.04 3.35 2.60 0 Subiculum, ventral part SUBv C57BL/6J 152994878 -4.04 3.50 2.60 0 Subiculum, ventral part SUBv Cux2-IRES-Cre 298795868 -4.72 3.40 2.20 0 Subiculum, ventral part SUBv Drd3-Cre_KI196 293701770 -4.16 3.80 3.00 0 Subiculum, ventral part SUBv Gad2-IRES-Cre 167513067 -2.70 0.56 1.92 0 Subiculum, ventral part SUBv Grik4-Cre 264945172 -4.00 3.40 2.60 0 Subiculum, ventral part SUBv Rbp4-Cre_KL100 299446445 -4.72 3.40 2.2, 2.6 0 Subiculum, ventral part SUBv Scnn1a-Tg3-Cre 268041088 -4.04 3.80 1.90 0 Subiculum, ventral part SUBv Syt17-Cre_NO14 286610216 -3.08 3.00 3.60 0 Subiculum, ventral part SUBv Tac1-IRES2-Cre 294314037 -4.72 3.40 2.20, 2.60 0 Sublaterodorsal nucleus SLD Crh-IRES-Cre (BL) 277853501 -5.52 0.88 2.71 0 Sublaterodorsal nucleus SLD Crh-IRES-Cre (BL) 278180500 -4.22 0.25 4.40 0 Submedial nucleus of the thalamus SMT Vipr2-Cre_KE2 268163228 -1.34 0.32 4.05 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 101 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Subparafascicular area SPA Calb2-IRES-Cre 184158996 -2.18 1.23 3.71 20 Subparafascicular nucleus, magnocellular part SPFm C57BL/6J 273025872 -1.22 0.30 4.15 0 Subparafascicular nucleus, magnocellular part SPFm Pdzk1ip1Cre_KD31 159258618 -2.30 0.25 3.90 0 Subparafascicular nucleus, magnocellular part SPFm Ppp1r17Cre_NL146 292480129 -2.06 0.25 4.15 0 Subparafascicular nucleus, parvicellular part SPFp C57BL/6J 127396051 -2.92 1.75 3.45 0 Subparafascicular nucleus, parvicellular part SPFp C57BL/6J 174583187 -3.28 2.00 3.20 0 Subparafascicular nucleus, parvicellular part SPFp Calb2-IRES-Cre 287880821 -2.92 1.75 3.45 0 Subparafascicular nucleus, parvicellular part SPFp Calb2-IRES-Cre 301063301 -2.92 1.75 3.45 0 Subparafascicular nucleus, parvicellular part SPFp Th-Cre_FI172 266501422 -2.92 1.75 3.45 0 Subparaventricular zone SBPV Oxtr-Cre_ON66 299408890 -0.58 0.20 4.75 0 Substantia innominata SI C57BL/6J 125436508 1.10 1.50 5.15 0 Substantia innominata SI C57BL/6J 273026584 0.62 1.20 4.90 0 Substantia innominata SI Chat-IRES-Cre 126711445 -0.58 1.75 4.50 0 Substantia innominata SI Chat-IRES-Cre 126841788 0.02 1.60 4.55 0 Substantia innominata SI Chrna2Cre_OE25 304762245 1.10 1.50 5.15 0 Substantia innominata SI Chrna2Cre_OE25 304970618 -0.94 2.25 4.47 0 Substantia innominata SI Crh-IRES-Cre (BL) 278179088 -0.94 2.25 4.47 0 Substantia innominata SI Drd3-Cre_KI196 300111087 -1.82 2.65 4.25 0 Substantia innominata SI Drd3-Cre_KI196 305026861 0.62 1.20 4.85 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 102 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Substantia innominata SI Efr3aCre_NO108 298835152 0.14 2.07 4.76 0 Substantia innominata SI Ntrk1-IRES-Cre 299404532 -0.58 1.75 4.50 0 Substantia innominata SI Slc17a6-IRESCre 302739608 0.62 1.20 4.85 0 Substantia nigra, compact part SNc Calb2-IRES-Cre 301062306 -1.70 1.40 4.85 0 Substantia nigra, compact part SNc Gad2-IRES-Cre 303534443 -3.28 1.50 4.30 0 Substantia nigra, compact part SNc Slc18a2Cre_OZ14 292958638 -3.08 1.25 4.15 0 Substantia nigra, compact part SNc Slc6a3-Cre 160539283 -3.08 1.25 4.08 0 Substantia nigra, reticular part SNr C57BL/6J 100141993 -3.28 1.50 4.30 0 Substantia nigra, reticular part SNr C57BL/6J 158914182 -3.08 1.25 4.30 0 Substantia nigra, reticular part SNr C57BL/6J 175263063 -3.40 1.60 4.60 0 Substantia nigra, reticular part SNr Pvalb-IRES-Cre 299895444 -3.28 1.50 4.30 0 Subthalamic nucleus STN A930038C07RikTg1-Cre 264697714 -1.70 1.40 4.85 0 Subthalamic nucleus STN C57BL/6J 146986331 -1.34 1.75 4.50 0 Subthalamic nucleus STN C57BL/6J 174788109 -1.82 2.05 4.25 0 Superior central nucleus raphe CS C57BL/6J 156929391 -4.36 0.30 4.50 0 Superior central nucleus raphe CS Slc18a2Cre_OZ14 300689439 -4.84 0.22 3.85 0 Superior colliculus, motor related SCm C57BL/6J 126523066 -4.48 0.50 1.85 0 Superior colliculus, motor related SCm C57BL/6J 126646502 -3.80 0.30 1.20 0 Superior colliculus, motor related SCm C57BL/6J 128001349 -4.36 1.25 1.20 0 Superior colliculus, motor related SCm C57BL/6J 146078721 -3.80 1.50 1.77 0 Superior colliculus, motor related SCm C57BL/6J 175158132 -3.80 1.50 2.10 0 Superior colliculus, motor related SCm Gad2-IRES-Cre 266646036 -2.92 1.25 2.76 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 103 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Superior colliculus, motor related SCm Nos1-CreERT2 305025440 -4.36 0.50 1.00 0 Superior colliculus, motor related SCm Pdzk1ip1Cre_KD31 167118084 -2.92 1.25 2.76 0 Superior colliculus, motor related SCm Pdzk1ip1Cre_KD31 182029881 -2.70 0.56 1.92 0 Superior colliculus, motor related SCm Pdzk1ip1Cre_KD31 183376269 -2.70 0.56 1.92 0 Superior colliculus, motor related SCm Ppp1r17Cre_NL146 278513131 -4.36 0.30 0.94 0 Superior colliculus, motor related SCm Ppp1r17Cre_NL146 292533477 -0.82 1.13 3.28 0 Superior colliculus, motor related SCm Ppp1r17Cre_NL146 307656580 -3.80 1.50 1.77 0 Superior colliculus, motor related SCm Ppp1r17Cre_NL146 307691605 -4.36 0.30 0.94 0 Superior colliculus, motor related SCm Pvalb-IRES-Cre 182613651 -4.36 0.50 2.01 0 Superior colliculus, motor related SCm Slc17a6-IRESCre 294175704 -2.80 0.25 2.40 0 Superior colliculus, motor related SCm Slc17a6-IRESCre 305426208 -3.16 1.60 2.85 0 Superior colliculus, sensory related SCs C57BL/6J 112827164 -4.36 0.30 0.94 0 Superior colliculus, sensory related SCs C57BL/6J 114754390 -3.52 0.60 1.07 0 Superior colliculus, sensory related SCs Gad2-IRES-Cre 292211743 -4.72 1.25 1.10 0 Superior colliculus, sensory related SCs Pdzk1ip1Cre_KD31 176900059 -3.52 0.60 1.25 0 Superior colliculus, sensory related SCs Ppp1r17Cre_NL146 278511717 -4.36 1.25 1.20 0 Superior colliculus, sensory related SCs Ppp1r17Cre_NL146 287459601 -3.80 0.30 1.20 0 Superior colliculus, sensory related SCs Rorb-IRES2-Cre 304338014 -3.52 0.60 1.25 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 104 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Superior olivary complex, lateral part SOCl Nxph4-2ACreERT2 287668550 0.00 calamus (-7.32 bregma) 0.05 0.20 0 Supplemental somatosensory area SSs A930038C07RikTg1-Cre 286834976 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs C57BL/6J 100149969 1.10 3.25, 3.00 1.24, 1.69 0 Supplemental somatosensory area SSs C57BL/6J 112514915 -0.70 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs C57BL/6J 113036264 -0.22 3.88, 3.38 1.65 0 Supplemental somatosensory area SSs C57BL/6J 117298988 -0.82 3.90 1.75 0 Supplemental somatosensory area SSs C57BL/6J 174360333 0.26 3.65 1.85 0 Supplemental somatosensory area SSs C57BL/6J 180717881 0.74 3.30 1.63 0 Supplemental somatosensory area SSs Chrna2Cre_OE25 297945448 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Cux2-IRES-Cre 278315824 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Cux2-IRES-Cre 287951098 -0.22 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs Cux2-IRES-Cre 297855879 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Efr3aCre_NO108 287996596 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Efr3aCre_NO108 301178953 -0.22 3.38, 3.88 1.66 0 Supplemental somatosensory area SSs Nr5a1-Cre 266175461 -0.22 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs Ntsr1Cre_GN220 159552290 -0.70 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs Ntsr1Cre_GN220 159750477 1.10 3.25, 3.00 1.90, 2.35 0 Supplemental somatosensory area SSs Oxtr-Cre_ON66 286838022 -0.22 3.40 3.25 0 Supplemental somatosensory area SSs Rbp4-Cre_KL100 168163498 -0.70 3.88, 3.38 1.66 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 105 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Supplemental somatosensory area SSs Rbp4-Cre_KL100 286314623 -0.22 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs Rorb-IRES2-Cre 301580339 -0.70 3.5, 4.0 1.70 0 Supplemental somatosensory area SSs Scnn1a-Tg3-Cre 257636467 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Slc18a2Cre_OZ14 268042502 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Slc18a2Cre_OZ14 287039061 -0.70 4.00, 3.50 1.70 0 Supplemental somatosensory area SSs Syt6-Cre_KI148 159508775 -0.70 3.88, 3.38 1.66 0 Supplemental somatosensory area SSs Syt6-Cre_KI148 299829181 -0.22 3.38, 3.88 1.66 0 Supplemental somatosensory area SSs Tlx3-Cre_PL56 303616833 -0.22 3.38, 3.88 1.66 0 Suprachiasmatic nucleus SCH Avp-IRES2-Cre 287665706 -0.34 0.20 5.60 0 Suprachiasmatic nucleus SCH Ppp1r17Cre_NL146 286727483 -0.34 0.20 5.60 0 Suprachiasmatic nucleus SCH Rorb-IRES2-Cre 304473503 -4.36 0.50 1.00 0 Suprachiasmatic nucleus SCH Vip-IRES-Cre 293431163 -0.34 0.20 5.60 0 Suprageniculate nucleus SGN Slc18a2Cre_OZ14 300688721 -3.16 2.10 2.85 0 Supramammillary nucleus SUM C57BL/6J 273055501 -2.35 0.13 5.30 0 Supramammillary nucleus SUMm Nos1-CreERT2 304947804 -2.80 0.25 4.90 0 Supramammillary nucleus, lateral part SUMl C57BL/6J 158314987 -2.80 0.25 4.90 0 Supramammillary nucleus, lateral part SUMl Hdc-Cre_IM1 157952778 -2.46 1.00 5.30 0 Supramammillary nucleus, lateral part SUMl Hdc-Cre_IM1 175736945 -2.46 1.00 5.30 0 Supramammillary nucleus, lateral part SUMl Nxph4-2ACreERT2 304720741 -2.70 0.13 5.20 0 Supraoptic nucleus SO Avp-IRES2-Cre 286726065 -0.46 1.15 5.45 0 Supraoptic nucleus SO Avp-IRES2-Cre 287666431 -0.46 1.15 5.45 0 Supraoptic nucleus SO Oxt-IRES-Cre 147790922 -0.58 1.13 5.40 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 106 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Supraoptic nucleus SO Oxt-IRES-Cre 147968866 -0.58 1.13 5.40 0 Supraoptic nucleus SO Oxt-IRES-Cre 178488152 -0.58 1.13 5.40 0 Taenia tecta, dorsal part TTd C57BL/6J 133286030 2.34 0.40 2.89 0 Taenia tecta, dorsal part TTd C57BL/6J 141601779 1.70 0.40 2.00 0 Taenia tecta, dorsal part TTd Cnnm2Cre_KD18 167029528 1.34 0.10 2.80 0 Taenia tecta, dorsal part TTd Kcnc2-Cre 176899332 2.34 0.40 2.89 0 Tegmental reticular nucleus TRN C57BL/6J 121145045 -4.16 0.25 4.90 0 Tegmental reticular nucleus TRN C57BL/6J 147135812 -4.16 0.25 5.15 0 Tegmental reticular nucleus TRN Crh-IRES-Cre (BL) 293752263 -4.72 0.25 4.40 0 Tegmental reticular nucleus TRN Gabrr3Cre_KC112 263976175 -4.16 0.25 5.60 0 Tegmental reticular nucleus TRN Gabrr3Cre_KC112 301875966 -4.04 0.25 5.90 0 Temporal association areas TEa A930038C07RikTg1-Cre 176429574 -4.36 4.00 1.25 0 Temporal association areas TEa A930038C07RikTg1-Cre 298350922 -4.36 4.25 1.35 0 Temporal association areas TEa C57BL/6J 114250546 -4.60 3.60 0.55 0 Temporal association areas TEa C57BL/6J 127089669 -4.16 3.85 0.90 0 Temporal association areas TEa C57BL/6J 157062358 0.62 2.90 3.75 0 Temporal association areas TEa Chrna2Cre_OE25 292208876 -4.36 4.25 1.35 0 Temporal association areas TEa Cux2-IRES-Cre 287953929 -4.60 3.80 0.45 30 Temporal association areas TEa Cux2-IRES-Cre 293470216 -4.36 4.00 1.25 0 Temporal association areas TEa Ntsr1Cre_GN220 159321806 -4.36 4.00 1.25 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 107 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Temporal association areas TEa Ntsr1Cre_GN220 170261951 -4.04 4.00 0.35, 0.75 30 Temporal association areas TEa Ntsr1Cre_GN220 298830868 -4.26 3.40 2.2, 2.6 0 Temporal association areas TEa Rbp4-Cre_KL100 166083557 -4.16 3.75 0.81 0 Temporal association areas TEa Rbp4-Cre_KL100 167027666 -4.36 4.00 1.25 0 Temporal association areas TEa Rbp4-Cre_KL100 298178204 -4.16 3.95 0.85 0 Temporal association areas TEa Syt6-Cre_KI148 156786939 -4.16 3.75 0.81 0 Temporal association areas TEa Syt6-Cre_KI148 158141324 -4.36 4.00 1.25 0 Temporal association areas TEa Tlx3-Cre_PL56 294516943 -4.36 4.00 1.25 0 Triangular nucleus of septum TRS C57BL/6J 125830911 -0.10 0.10 2.30 0 Tuberal nucleus TU Avp-IRES2-Cre 267396430 -0.58 1.15 5.50 0 Tuberal nucleus TU Avp-IRES2-Cre 267397226 -0.58 1.15 5.50 0 Tuberal nucleus TU Esr1-2A-Cre 176886958 -1.50 0.78 5.75 0 Tuberal nucleus TU Esr1-2A-Cre 264320076 -1.50 0.78 5.76 0 Tuberomammillary nucleus, ventral part TMv Hdc-Cre_IM1 157952068 -2.46 0.55 5.65 0 Ventral anterior-lateral complex of the thalamus VAL C57BL/6J 100142569 -0.82 1.13 3.28 0 Ventral anterior-lateral complex of the thalamus VAL C57BL/6J 113884251 -0.70 1.53 3.48 0 Ventral anterior-lateral complex of the thalamus VAL Gal-Cre_KI87 156393801 -0.58 3.40 4.94 40 Ventral anterior-lateral complex of the thalamus VAL Grik4-Cre 300237470 -0.70 1.53 3.48 0 Ventral anterior-lateral complex of the thalamus VAL Prkcd-GluClaCFP-IRES-Cre 292321278 -0.82 1.13 3.28 0 Ventral anterior-lateral complex of the thalamus VAL Slc17a6-IRESCre 310193233 -1.34 0.85 3.97 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 108 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Ventral auditory area AUDv C57BL/6J 112881858 -2.80 4.40 1.60 0 Ventral auditory area AUDv Tlx3-Cre_PL56 303582161 -2.46 4.35 0.85 0 Ventral cochlear nucleus VCO C57BL/6J 272825299 -5.52 2.50 3.65 0 Ventral cochlear nucleus VCO Ntrk1-IRES-Cre 265135682 -5.52 2.50 3.65 0 Ventral cochlear nucleus VCO Pvalb-IRES-Cre 167211503 -5.52 2.50 3.65 0 Ventral medial nucleus of the thalamus VM C57BL/6J 174736554 -1.46 0.80 4.25 0 Ventral medial nucleus of the thalamus VM C57BL/6J 180707817 -1.46 0.80 4.25 0 Ventral medial nucleus of the thalamus VM Cck-IRES-Cre 277849256 -3.80 0.04 2.85 0 Ventral medial nucleus of the thalamus VM Cck-IRES-Cre 306444486 -1.50 0.35 5.30 0 Ventral medial nucleus of the thalamus VM Gabrr3Cre_KC112 170859382 -1.34 0.95 4.55 0 Ventral medial nucleus of the thalamus VM Ppp1r17Cre_NL146 268205344 -1.34 0.85 3.97 0 Ventral medial nucleus of the thalamus VM Prkcd-GluClaCFP-IRES-Cre 267929554 -1.34 0.85 3.97 0 Ventral medial nucleus of the thalamus VM Prkcd-GluClaCFP-IRES-Cre 278067445 -1.34 0.32 4.05 0 Ventral part of the lateral geniculate complex LGv C57BL/6J 147212977 -2.30 2.55 3.00 0 Ventral part of the lateral geniculate complex LGv Pdzk1ip1Cre_KD31 157765542 -2.30 2.55 3.00 0 Ventral part of the lateral geniculate complex LGv Ppp1r17Cre_NL146 278398949 -2.80 2.85 3.00 0 Ventral part of the lateral geniculate complex LGv Slc32a1-IRESCre 267538006 -2.46 2.60 2.36 0 Ventral part of the lateral geniculate complex LGv Sst-IRES-Cre 299623794 -2.30 2.55 3.00 0 Ventral posterolateral nucleus of the thalamus VPL C57BL/6J 158375425 -1.70 1.90 3.40 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 109 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Ventral posterolateral nucleus of the thalamus VPL Grik4-Cre 287446625 -0.70 1.53 3.48 0 Ventral posterolateral nucleus of the thalamus VPL Grik4-Cre 287447332 -1.22 2.00 3.09 0 Ventral posterolateral nucleus of the thalamus VPL Grik4-Cre 301877386 -1.22 2.00 3.09 0 Ventral posterolateral nucleus of the thalamus VPL Scnn1a-Tg2-Cre 156202272 -1.70 1.90 3.40 0 Ventral posteromedial nucleus of the thalamus VPM C57BL/6J 100141223 -1.34 0.85 3.97 0 Ventral posteromedial nucleus of the thalamus VPM C57BL/6J 180601025 -1.46 2.20 3.09 0 Ventral posteromedial nucleus of the thalamus VPM Gal-Cre_KI87 182515576 -1.82 1.50 3.25 0 Ventral posteromedial nucleus of the thalamus VPM Gal-Cre_KI87 278070717 -2.00 2.15 2.60 0 Ventral posteromedial nucleus of the thalamus VPM Ppp1r17Cre_NL146 268206050 -1.70 1.90 3.40 0 Ventral posteromedial nucleus of the thalamus VPM Ppp1r17Cre_NL146 268399868 -1.82 1.60 3.30 0 Ventral posteromedial nucleus of the thalamus VPM Scnn1a-Tg2-Cre 156202979 -1.82 1.50 3.25 0 Ventral posteromedial nucleus of the thalamus VPM Slc17a6-IRESCre 312240825 -1.70 1.90 3.40 0 Ventral posteromedial nucleus of the thalamus, parvicellular part VPMpc Ppp1r17Cre_NL146 278509488 -1.94 0.90 5.00 0 Ventral posteromedial nucleus of the thalamus, parvicellular part VPMpc Scnn1a-Tg2-Cre 162018169 -2.06 0.45 4.00 0 Ventral posteromedial nucleus of the thalamus, parvicellular part VPMpc Scnn1a-Tg2-Cre 162018879 -1.94 1.10 4.00 0 Ventral premammillary nucleus PMv Avp-IRES2-Cre 267398651 -1.58 0.75 5.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 110 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Ventral premammillary nucleus PMv Lepr-IRES-Cre 167656152 -2.46 0.55 5.65 0 Ventral premammillary nucleus PMv Slc6a3-Cre 263780018 -2.46 0.55 5.65 0 Ventral premammillary nucleus PMv Tac1-IRES2-Cre 299654968 -1.46 0.39 5.50 0 Ventral premammillary nucleus PMv Th-Cre_FI172 286728896 -1.70 0.20 5.90 0 Ventral tegmental area VTA C57BL/6J 126710740 -2.46 0.55 5.65 0 Ventral tegmental area VTA C57BL/6J 127796728 -2.55 0.13 4.55 0 Ventral tegmental area VTA Cck-IRES-Cre 171021829 -3.28 0.36 4.13 0 Ventral tegmental area VTA Chrna2Cre_OE25 278178382 -3.52 0.28 4.30 0 Ventral tegmental area VTA Erbb4-2ACreERT2 127867804 -3.28 0.36 4.13 0 Ventral tegmental area VTA Erbb4-2ACreERT2 165975096 -3.28 0.36 4.13 0 Ventral tegmental area VTA Gabrr3Cre_KC112 300166697 -2.80 0.25 4.90 0 Ventral tegmental area VTA Nos1-CreERT2 304720034 -2.46 0.55 5.65 0 Ventral tegmental area VTA Pdzk1ip1Cre_KD31 166054222 -3.28 0.36 4.13 0 Ventral tegmental area VTA Slc17a6-IRESCre 302087552 -2.30 0.25 4.37 0 Ventral tegmental area VTA Slc18a2Cre_OZ14 287492899 -2.80 0.80 5.15 0 Ventral tegmental area VTA Slc18a2Cre_OZ14 301732962 -3.28 0.36 4.13 0 Ventral tegmental area VTA Slc6a3-Cre 160540751 -3.28 0.36 4.13 0 Ventral tegmental area VTA Syt17-Cre_NO14 127798146 -3.28 0.36 4.13 0 Ventral tegmental area VTA Th-Cre_FI172 304337288 -3.28 0.36 4.13 0 Ventral tegmental area VTA Th-IRES-CreER 156314762 -3.28 0.36 4.13 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 111 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Ventromedial hypothalamic nucleus VMH Adcyap1-2A-Cre 303708513 -1.46 0.39 5.50 0 Ventromedial hypothalamic nucleus VMH C57BL/6J 157549402 -0.70 0.37 5.40 0 Ventromedial hypothalamic nucleus VMH C57BL/6J 175106769 -0.70 0.40 5.46 0 Ventromedial hypothalamic nucleus VMH C57BL/6J 277615922 -0.70 0.40 5.55 0 Ventromedial hypothalamic nucleus VMH Erbb4-2ACreERT2 277854916 -1.70 0.20 5.90 0 Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 176888661 -1.50 0.78 5.75 0 Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 264248605 -1.50 0.78 5.76 0 Ventromedial hypothalamic nucleus VMH Esr1-2A-Cre 264319363 -1.50 0.78 5.76 0 Ventromedial hypothalamic nucleus VMH Fezf1-2A-dCre 267540168 -1.46 0.39 5.50 0 Ventromedial hypothalamic nucleus VMH Fezf1-2A-dCre 292211026 -1.46 0.39 5.50 0 Ventromedial hypothalamic nucleus VMH Ins2-Cre 286319033 -1.46 0.39 5.50 0 Ventromedial hypothalamic nucleus VMH Nr5a1-Cre 114290225 -1.46 0.39 5.30 0 Ventromedial hypothalamic nucleus VMH Nr5a1-Cre 182337561 -1.46 0.39 5.30 0 Ventromedial hypothalamic nucleus VMH Slc17a6-IRESCre 286556208 -1.50 0.35 5.30 0 Ventromedial hypothalamic nucleus VMH Sst-IRES-Cre 304948510 -1.58 0.75 5.75 0 Visceral area VISC C57BL/6J 180074890 -1.22 4.00 2.60 0 Visceral area VISC C57BL/6J 180917660 -0.58 4.20 2.15 0 Visceral area VISC Rbp4-Cre_KL100 249402048 1.10 3.25, 3.00 1.90, 2.35 0 Visceral area VISC Syt6-Cre_KI148 177783918 1.10 3.25, 3.00 1.90, 2.35 0 Zona incerta ZI C57BL/6J 113095845 -2.18 1.75 4.12 0 Zona incerta ZI C57BL/6J 126190743 -1.70 1.40 4.45 0 Zona incerta ZI C57BL/6J 127797441 -1.34 0.95 4.55 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 112 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Zona incerta ZI C57BL/6J 157063074 -3.52 2.50 1.35 0 Zona incerta ZI C57BL/6J 175018829 -2.70 1.50 3.50 0 Zona incerta ZI Cart-Tg1-Cre 266174751 -1.50 0.35 5.20 0 Zona incerta ZI Drd3-Cre_KI196 304858700 -2.18 1.75 4.12 0 Zona incerta ZI Gabrr3Cre_KC112 170263370 -1.70 1.40 4.45 0 Zona incerta ZI Gabrr3Cre_KC112 170858675 -2.18 1.75 4.12 0 Zona incerta ZI Gad2-IRES-Cre 156315468 -1.34 0.95 4.55 0 Zona incerta ZI Gad2-IRES-Cre 286662551 -2.18 1.75 4.12 0 Zona incerta ZI Gad2-IRES-Cre 305321883 -1.70 1.40 4.85 0 Zona incerta A13 Lypd6Cre_KL156 299760587 -1.34 1.00 4.84 0 Zona incerta ZI Pvalb-IRES-Cre 301539438 -2.18 1.75 4.12 0 Zona incerta ZI Slc17a6-IRESCre 168663472 -1.70 1.40 4.45 0 Zona incerta ZI Slc32a1-IRESCre 171065906 -2.18 1.75 4.12 0 Zona incerta ZI Slc32a1-IRESCre 171066613 -1.34 0.95 4.55 0 Zona incerta ZI Slc32a1-IRESCre 305379705 -1.70 1.40 4.85 0 Zona incerta ZI Tac1-IRES2-Cre 300923916 -0.80 0.25 4.85 0 Zona incerta ZI Th-Cre_FI172 306270474 -1.34 0.95 4.55 0 * For the majority of target sites, the anterior/posterior (AP) coordinates are referenced from Bregma, the medial/lateral (ML) coordinates are distance from midline at Bregma, and dorsal/ventral (DV) coordinates are measured from the pial surface of the brain. For several of the caudal-most medullary nuclei (e.g. gracile nucleus and spinal nucleus of the trigeminal, caudal part), the calamus (at the floor of the 4th ventricle) is used as a registration point instead of Bregma. MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 113 of 117 alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Table 2. Stereotaxic coordinates used for BDA vs. rAAV comparison. Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Anterior olfactory nucleus AON C57BL/6J 100142693 2.96 1.14 2.67 0 Anterior olfactory nucleus AON C57BL/6J 100144288 2.96 1.14 2.67 0 Anterior olfactory nucleus AON C57BL/6J 100147358 2.96 1.14 2.67 0 Caudoputamen CP C57BL/6J 100142699 -0.34 1.90 3.40 0 Caudoputamen CP C57BL/6J 100142293 0.74 1.75 2.60 0 Caudoputamen CP C57BL/6J 100144295 0.74 1.75 2.60 0 Caudoputamen CP C57BL/6J 100145836 0.74 1.75 2.60 0 Caudoputamen CP B6129SF1/J 112311239 -0.34 1.90 3.40 0 Caudoputamen CP B6129SF1/J 159609527 0.74 1.75 2.60 0 Caudoputamen CP B6129SF1/J 183568601 0.74 1.75 2.60 0 Field CA1 CA1 C57BL/6J 100141775 -1.94 1.00 1.30 0 Field CA1 CA1 C57BL/6J 100141772 -1.94 1.00 1.30 0 Field CA1 CA1 B6129SF1/J 113067695 -1.94 1.00 1.30 0 Gigantocellular reticular nucleus GRN C57BL/6J 100142687 -7.20 0.50 4.75 0 Globus pallidus, external segment GPe C57BL/6J 100141804 -0.34 1.90 3.40 0 Inferior colliculus, external nucleus ICe C57BL/6J 100145841 -4.36 1.59 1.87 0 Intermediate reticular nucleus IRN C57BL/6J 100144286 -7.20 0.50 4.75 0 Kolliker-Fuse subnucleus KF C57BL/6J 100142301 -5.20 1.40 3.58 0 Lateral hypothalamic area LHA C57BL/6J 100141800 -1.06 1.00 4.75 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 114 of 117 Experiment ID AP ML DV Angle° alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Lateral hypothalamic area LHA C57BL/6J 100147352 -1.06 1.12 4.88 0 Lateral hypothalamic area LHA C57BL/6J 100142700 -1.06 1.00 4.75 0 Lateral hypothalamic area LHA B6129SF1/J 113066020 -1.06 1.00 4.75 0 Lateral hypothalamic area LHA C57BL/6J 159616564 -0.70 1.12 5.00 0 Lateral posterior nucleus of the thalamus LP C57BL/6J 112296535 -2.30 2.00 2.45 0 Lateral posterior nucleus of the thalamus LP C57BL/6J 100141798 -2.30 2.00 2.45 0 Lateral septal nucleus LS B6129SF1/J 100147797 0.14 0.50 2.80 0 Lateral septal nucleus LS C57BL/6J 159617389 0.14 0.50 2.80 0 Lateral septal nucleus, caudal (caudodorsal) part LSc C57BL/6J 112312484 0.14 0.50 2.80 0 Lateral septal nucleus, rostral (rostroventral) part LSr C57BL/6J 100142294 0.14 0.50 2.80 0 Lobules IV-V CUL 4,5 C57BL/6J 100145843 -5.88 0.50 0.40 0 Lobules IV-V CUL4, 5 C57BL/6J 100147373 -6.24 0.50 0.94 0 Lobules IV-V CUL4, 5 C57BL/6J 100147369 -6.24 0.50 0.94 0 Lobules IV-V CUL4, 5 C57BL/6J 100147375 -6.24 0.50 0.94 0 Medullary reticular nucleus, ventral part MDRNv C57BL/6J 100145829 -7.20 0.50 4.75 0 Midbrain reticular nucleus MRN C57BL/6J 100142300 -3.40 0.75 3.60 0 Midbrain reticular nucleus MRN C57BL/6J 100143833 -3.40 0.75 3.60 0 Midbrain reticular nucleus MRN C57BL/6J 100145833 -3.40 0.75 3.60 0 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 115 of 117 Experiment ID AP ML DV Angle° alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Midbrain reticular nucleus MRN C57BL/6J 100142704 -3.28 1.50 4.30 0 Posterior complex of the thalamus PO C57BL/6J 112297892 -1.82 1.50 3.25 0 Posterior complex of the thalamus PO B6129SF1/J 113066858 -1.82 1.50 3.25 0 Primary motor area MOp C57BL/6J 100141268 1.54 1.60 0.40, 0.80 0 Primary motor area MOp C57BL/6J 100145496 1.54 1.60 0.40, 0.80 0 Primary motor area MOp C57BL/6J 100142689 1.54 1.60 0.40, 0.80 0 Primary motor area MOp B6129SF1/J 100147371 1.54 1.60 0.40, 0.80 0 Primary motor area MOp C57BL/6J 159613261 1.54 1.60 0.40, 0.80 0 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 100141261 -1.46 3.25 0.40, 0.80 20 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 100142701 -1.46 3.25 0.35, 0.80 20 Primary somatosensory area, barrel field SSp-bfd C57BL/6J 159611609 -1.46 3.25 0.40, 0.80 20 Primary somatosensory area, trunk SSp-tr C57BL/6J 100147356 -1.46 3.25 0.40, 0.80 20 Primary somatosensory area, trunk SSp-tr B6129SF1/J 159610371 -1.46 3.25 0.40, 0.80 20 Primary visual area VISp C57BL/6J 100141263 -4.16 2.75 0.45 10 Primary visual area VISp C57BL/6J 100141777 -4.16 2.75 0.45 10 Primary visual area VISp C57BL/6J 100144292 -4.16 2.75 0.45 10 Primary visual area VISp C57BL/6J 159609113 -4.16 2.75 0.45 10 Primary visual area VISp C57BL/6J 159614086 -4.16 2.75 0.45 10 MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 116 of 117 Experiment ID AP ML DV Angle° alleninstitute.org brain-map.org Allen Mouse Brain Connectivity Atlas TECHNICAL WHITE PAPER Brain region (primary structure infected by rAAV) Reference atlas acronym Mouse strain Experiment ID AP ML DV Angle° Primary visual area VISp B6129SF1/J 159612434 -4.16 2.75 0.45 10 Septofimbrial nucleus SF C57BL/6J 100141266 0.14 0.50 2.80 0 Septofimbrial nucleus SF B6129SF1/J 112296088 -1.46 3.25 0.40, 0.80 20 Subiculum SUB C57BL/6J 100142710 -2.92 1.17 1.40 0 Subiculum SUB C57BL/6J 100145827 -2.92 1.17 1.40 0 Subiculum SUB C57BL/6J 112314965 -2.92 1.17 1.40 0 Substantia innominata SI B6129SF1/J 113071071 -1.22 2.75 3.80 0 Substantia nigra, compact part SNc C57BL/6J 100147802 -3.28 1.50 4.30 0 Substantia nigra, reticular part SNr C57BL/6J 100142698 -3.28 1.50 4.30 0 Substantia nigra, reticular part SNr C57BL/6J 112302860 -3.28 1.50 4.30 0 Superior colliculus, motor related SCm C57BL/6J 100143837 -4.36 1.59 1.87 0 Superior colliculus, motor related SCm C57BL/6J 100142302 -4.36 1.59 1.87 0 Superior colliculus, motor related SCm B6129SF1/J 113072328 -4.36 1.59 1.87 0 Superior colliculus, sensory related SCs C57BL/6J 100142706 -4.36 0.50 0.42 0 Ventral posteromedial nucleus of the thalamus VPM C57BL/6J 100143831 -1.82 1.50 3.25 0 Ventral posteromedial nucleus of the thalamus VPM C57BL/6J 100149111 -1.82 1.50 3.25 0 * For most cases presented, the anatomical area(s) of tracer uptake are well matched. However, there are cases with considerable differences in the uptake area between BDA and rAAV due to uneven infection or leakage along the needle tract into neighboring anatomical regions. In such cases, the primary structure infected by rAAV or BDA is listed separately on the website. MARCH 2016 v.9 Injection Sites and Stereotaxic Coordinates page 117 of 117 alleninstitute.org brain-map.org