Mouse Motor Cortex Reference Explorer

Annotation Markers

class

Label	Expanded Label	OBO Ontology ID	Markers
Glutamatergic	Glutamatergic neuron	glutamatergic neuron	Celf2, Ptprd, Arpp21, Sv2b, Pcsk2, Phactr1, Kalrn, Nrg1, Ano3, Satb2
Non-Neuronal	Non-neuronal cell	animal cell	Zbtb20, Qk, Cst3, Nfia, Apoe, Ptn, Maml2, Dock1, Cd81, Gab1
GABAergic	GABAergic neuron	GABAergic neuron	Grip1, Galntl6, Gad1, Gad2, Dlx6os1, Cntnap2, Gm26905, Kcnmb2, Kcnip1, Erbb4

subclass

Label	Expanded Label	OBO Ontology ID	Markers
Astro	Astrocyte	astrocyte	Gpc5, Slc1a2, Slc1a3, Apoe, Wdr17, Plpp3, Rorb, Rmst, Slc4a4, Htra1
Endo	Endothelial cell	endothelial cell	Flt1, Slco1a4, Adgrl4, Ly6c1, Slc2a1, Klf2, Mecom, Bsg, Ly6a, Pltp
L2/3 IT	Layer 2-3 glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	Lingo2, Dscaml1, Gpc6, Fam19a1, Lrrtm4, Slit3, Cux2, Unc5d, Fstl4, Car10
L5 ET	Layer 5 glutamatergic neuron, extratelencephalon-projecting	glutamatergic neuron	Fam19a1, Tox, Sgcz, Robo1, Galntl6, Gm2164, Dscaml1, Gm28928, Pex5l, Ralyl
L5 IT	Layer 5 glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	Car10, Ncam2, Galntl6, Cdh12, Hs3st4, Gpc6, Unc5d, Tenm4, Ptprd, Hs6st3
L5/6 NP	Layer 5-6 glutamatergic neuron, near-projecting	glutamatergic neuron	Tshz2, Gm26883, Nxph1, Vwc2l, Grik1, Olfm3, Kirrel3, Mgat4c, Hs6st3, Dcc
L6 CT	Layer 6 glutamatergic neuron, corticothalamic-projecting	glutamatergic neuron	Hs3st4, Chgb, Garnl3, Kctd16, Zfpm2, Foxp2, Mgat4c, Gm28928, Cdh18, Tle4
L6 IT	Layer 6 glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	C1ql3, Cdh13, Il1rapl2, Zfp804b, Dscaml1, Slit3, Galnt14, Nell2, Ak5, Cck
L6 IT Car3	Layer 6 Car3+ glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	Tfap2d, Oprk1, Smoc2, Car12, Nr4a2, Lxn, Gm32647, Col11a1, Sstr2, 6530403H02Rik
L6b	Layer 6b glutamatergic neuron	glutamatergic neuron	Ctgf, Cdh18, Hs3st4, Kcnab1, Gm28928, Svil, Inpp4b, Zfpm2, Sdk2, Tle4
Lamp5	Lamp5+ GABAergic neuron	GABAergic neuron	Npy, Nxph1, Fgf13, Ptprm, Reln, Gad2, Unc5d, Alk, Unc5c, Lamp5
Meis2	Meis2+ GABAergic neuron	GABAergic neuron	Igfbpl1, Draxin, Cd1d1, Sp8, Cd24a, Lockd, St8sia2, Gm29260, Gm17750, Meis2
Micro-PVM	microglia / perivascular macrophage	perivascular macrophage	Inpp5d, Hexb, Tgfbr1, C1qa, Ctss, C1qb, Zfhx3, C1qc, Selplg, Cx3cr1
Oligo	oligodendrocyte	oligodendrocyte	Plp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Mag
OPC	oligodendrocyte precursor cell	oligodendrocyte precursor cell	Lhfpl3, Vcan, Tnr, Ptprz1, Gm4876, Xylt1, Pdgfra, Epn2, Cacng4, Megf11
Peri	pericyte	brain pericyte	Atp13a5, Vtn, Cald1, Ebf1, Abcc9, Dlc1, Pdgfrb, Tbx3os1, Pde8b, Slc38a11
Pvalb	Pvalb+ GABAergic neuron	GABAergic neuron	Kcnc2, Erbb4, Sox5, Il1rapl2, Fam19a2, Cntnap5c, Lrrc4c, Btbd11, Kcnh7, Pvalb
SMC	smooth muscle cell	smooth muscle cell	Acta2, Map3k7cl, Gm6249, Myh11, Tagln, Pdlim3, Ephx3, Olfr558, Crip1, Tbx2
Sncg	Sncg+ GABAergic neuron	GABAergic neuron	Adarb2, Cnr1, Megf10, Cadps2, Col25a1, Col19a1, Grip1, Sgcd, Slc44a5, Sncg
Sst	Sst+ GABAergic neuron	GABAergic neuron	Sst, Grin3a, Nxph1, Galntl6, Rgs6, Sox6, Mgat4c, Synpr, Cacna2d3, Grm1
Sst Chodl	Sst+ Chodl+ GABAergic neuron	GABAergic neuron	Nos1, Crhbp, Ndst4, Tacr1, 9330158H04Rik, Chodl, Fndc1, Stac, Bace2, Gabrg1
Vip	Vip+ GABAergic neuron	GABAergic neuron	Vip, Cacna1a, Adarb2, Limch1, Synpr, Cntn4, Crh, Sdk1, Igf1, Tac2
VLMC	vascular lepotomeningeal cell	brain pericyte	Ptgds, Bnc2, Cped1, Slc7a11, Bmp6, Apod, Mgp, Eya2, Ranbp3l, Adam12

cluster

Label	Expanded Label	OBO Ontology ID	Markers
Astro Aqp4_Gfap	Aqp4+ Gfap+ Astrocyte	astrocyte	Gpc5, Myoc, Slc1a2, Fxyd6, Slc1a3, Nrp2, Slc6a6, Apoe, Aqp4, Gfap
Astro Aqp4_Slc7a10	Aqp4+ Slc7a10+ Astrocyte	astrocyte	Lsamp, Gpc5, Slc1a2, Luzp2, Slc1a3, Apoe, Cadm2, Rora, Aqp4, Slc7a10
Astro_Top2a	Top2a+ Astrocyte	astrocyte	Igfbpl1, Gpc5, Mki67, Slc1a2, Myt1, Slc1a3, Apoe, E2f2, E2f7, Top2a
Endo	Endothelial cell	endothelial cell	Flt1, Slco1a4, Adgrl4, Ly6c1, Slc2a1, Klf2, Mecom, Bsg, Ly6a, Pltp
L2/3 IT_1	Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Adamts2, Lingo2, 6530403H02Rik, Dscaml1, Gpc6, Rhbdl3, 5730522E02Rik, Fam19a1, Arhgef28, Lrrtm4
L2/3 IT_2	Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Cntnap5c, Lingo2, Epha6, Dscaml1, Fras1, Gpc6, Fam19a1, Cdh13, Lrrtm4, Lsamp
L2/3 IT_3	Layer 2-3 glutamatergic neuron, intratelencephalon-projecting_3	glutamatergic neuron	Lingo2, Cdh12, Dscaml1, Sorcs3, Gpc6, Cntn4, Fam19a1, Pcdh9, Sorcs1, Lrrtm4
L5 ET_1	Layer 5 glutamatergic neuron, extratelencephalon-projecting_1	glutamatergic neuron	St6galnac5, Fam19a1, Tox, St6galnac3, Pigk, Sgcz, Robo1, Crym, Galntl6, Zfp804b
L5 ET_2	Layer 5 glutamatergic neuron, extratelencephalon-projecting_2	glutamatergic neuron	Fam19a1, Vwc2l, Tshz2, Tox, Sgcz, Gm26883, Erg, Robo1, Cdh18, Galntl6
L5 ET_3	Layer 5 glutamatergic neuron, extratelencephalon-projecting_3	glutamatergic neuron	Fam19a1, Gpc5, Tox, Galnt17, Lingo2, Sgcz, Stxbp6, Robo1, Spock1, Galntl6
L5 ET_4	Layer 5 glutamatergic neuron, extratelencephalon-projecting_4	glutamatergic neuron	Grin3a, Fam19a1, Olfm3, Tox, Sgcz, Tmtc2, Kctd8, Robo1, Galntl6, Lrp1b
L5 IT Pld5_1	Pld5+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Zfp804a, Car10, Ncam2, Cdh18, Galntl6, Pld5, Cdh12, Ptprt, Arhgap31, Hs3st4
L5 IT Pld5_2	Pld5+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Car10, Cdh9, Bcl11b, Ncam2, Galntl6, Dscaml1, Cwh43, Cdh12, Rxfp1, Pld5
L5 IT Rspo1_1	Rspo1+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Car10, Lingo2, Ncam2, Cux2, Galntl6, Cux1, Prr16, Cdh12, Brinp3, Rspo1
L5 IT Rspo1_2	Rspo1+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Car10, Zfp804b, Ncam2, Cntn5, Cdh8, Galntl6, Cdh12, Cpne4, Tnnc1, Rspo1
L5 IT S100b_1	S100b+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Il1rapl2, Car10, Deptor, Ncam2, Galntl6, Pde1a, AC129186.1, Cdh12, Grik3, S100b
L5 IT S100b_2	S100b+ Layer 5 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Car10, Cdh9, Ncam2, Rspo2, Galntl6, Blnk, Cdh12, AC129186.1, Gpc6, S100b
L5/6 NP CT	Layer 5-6 glutamatergic neuron, near-projecting_CT	glutamatergic neuron	Tshz2, Ephb1, Ankrd33b, Gm26883, Kctd8, Nxph1, Gm28928, Vwc2l, Grik1, Neto1
L5/6 NP_1	Layer 5-6 glutamatergic neuron, near-projecting_1	glutamatergic neuron	Hapln1, Tshz2, Gm26883, Cadps2, Nxph1, Rbfox1, Vwc2l, Il1rap, Grik1, Tmem132d
L5/6 NP_2	Layer 5-6 glutamatergic neuron, near-projecting_2	glutamatergic neuron	Tshz2, Stxbp6, Gm26883, Sv2c, Zeb2, Nxph1, Vwc2l, Gpc6, Grik1, Sema3e
L5/6 NP_3	Layer 5-6 glutamatergic neuron, near-projecting_3	glutamatergic neuron	Cntn6, Tshz2, Gm26883, Inpp4b, Kcnab1, Nxph1, Cntnap5b, Vwc2l, Chrm2, Grik1
L6 CT Cpa6	Cpa6+ Layer 6 glutamatergic neuron, corticothalamic-projecting	glutamatergic neuron	Hs3st4, Dscaml1, Chgb, Chrm3, Garnl3, Nfia, Kctd16, Kcnj6, Zfpm2, Cpa6
L6 CT Gpr139	Gpr139+ Layer 6 glutamatergic neuron, corticothalamic-projecting	glutamatergic neuron	Hs3st4, Gal, Mdga1, Chgb, Gpr139, Garnl3, Gm26719, Kctd16, Anxa4, Zfpm2
L6 CT Grp	Grp+ Layer 6 glutamatergic neuron, corticothalamic-projecting	glutamatergic neuron	Slc24a3, Hs3st4, Chgb, Ntm, Garnl3, Plcxd3, Kctd16, Tox, Meis2, Grp
L6 CT Kit_1	Kit+ Layer 6 glutamatergic neuron, corticothalamic-projecting_1	glutamatergic neuron	Hs3st4, Sostdc1, Nts, Chgb, Garnl3, Rmst, Kctd16, Kit, Zfpm2, Gm29114
L6 CT Kit_2	Kit+ Layer 6 glutamatergic neuron, corticothalamic-projecting_2	glutamatergic neuron	Hs3st4, Cobll1, Chgb, Dkk2, Garnl3, Kit, Rmst, Kctd16, Gm26883, Zfpm2
L6 CT Pou3f2	Pou3f2+ Layer 6 glutamatergic neuron, corticothalamic-projecting	glutamatergic neuron	Nxph2, Hs3st4, Gm28175, Chgb, Garnl3, Gm10635, Kctd16, Ntm, Kcnc2, Pou3f2
L6 IT Car3	Car3+ glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	C1ql3, Cdh13, Il1rapl2, Zfp804b, Dscaml1, Slit3, Galnt14, Nell2, Ak5, Car3
L6 IT_1	Layer 6 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Brinp3, C1ql3, Cdh13, Fst, Il1rapl2, Negr1, Efna5, Zfp804b, Plcxd3, Dscaml1
L6 IT_2	Layer 6 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Tfap2d, Cdh9, Pcdh7, Oprk1, Dcc, Smoc2, Cplx2, Car12, Chrm2, Nr4a2
L6b Col6a1	Col6a1+ Layer 6b glutamatergic neuron	glutamatergic neuron	Ctgf, Bmpr1b, Cdh18, Foxp2, Egfem1, Hs3st4, Kcnab1, Tcf4, Gm28928, Col6a1
L6b Kcnip1	Kcnip1+ Layer 6b glutamatergic neuron	glutamatergic neuron	Ctgf, Gm42557, Cdh18, Rxfp2, Kcnip1, Hs3st4, Kcnab1, 9530026P05Rik, Hcrtr2, Gm28928
L6b Ror1	Ror1+ Layer 6b glutamatergic neuron	glutamatergic neuron	Ctgf, Fbxl7, Kirrel3, Cdh18, Hs3st4, Fam19a5, Ptn, Kcnab1, Tox, Ror1
L6b Shisa6_1	Shisa6+ Layer 6b glutamatergic neuron_1	glutamatergic neuron	Ctgf, Shisa6, Thsd7b, Cdh18, Hs3st4, Kcnab1, Svil, Gm28928, Zfpm2, Inpp4b
L6b Shisa6_2	Shisa6+ Layer 6b glutamatergic neuron_2	glutamatergic neuron	Ctgf, Brinp3, Sema3e, Cdh18, Trhde, Hs3st4, Kcnab1, Il1rapl1, March1, Shisa6
Lamp5 Egln3_1	Lamp5+ Egln3+ GABAergic neuron_1	GABAergic neuron	Npy, Itga8, Nxph1, Egln3, Fgf13, Fam19a1, Ptprm, Fbn2, AC154782.1, Lamp5
Lamp5 Egln3_2	Lamp5+ Egln3+ GABAergic neuron_2	GABAergic neuron	Npy, D030045P18Rik, Nxph1, Crim1, Fgf13, Nrg1, Cdh18, Ptprm, Lamp5, Egln3
Lamp5 Egln3_3	Lamp5+ Egln3+ GABAergic neuron_3	GABAergic neuron	Ntn1, Npy, Nxph1, Dcc, Trpc4, Fgf13, Ndst4, Ptprm, Lamp5, Egln3
Lamp5 Lhx6	Lamp5+ Lhx6+ GABAergic neuron	GABAergic neuron	Npy, Lhx6, Cntnap3, Nxph1, Fgf13, Tacr1, Ptprm, Myo5b, Reln, Lamp5
Lamp5 Pax6	Lamp5+ Pax6+ GABAergic neuron	GABAergic neuron	Npy, Pax6, Nxph1, Npsr1, Scrg1, Fgf13, Gm16083, Ptprm, Reln, Lamp5
Lamp5 Pdlim5_1	Lamp5+ Pdlim5+ GABAergic neuron_1	GABAergic neuron	Cntn5, Npy, Nxph1, Cntn6, Fgf13, Pde4b, Ptprm, Grid1, Lamp5, Pdlim5
Lamp5 Pdlim5_2	Lamp5+ Pdlim5+ GABAergic neuron_2	GABAergic neuron	Npy, Ndnf, Nxph1, Cntn5, Fgf13, Sema3e, Ptprm, Grik1, Lamp5, Pdlim5
Lamp5 Slc35d3	Lamp5+ Slc35d3+ GABAergic neuron	GABAergic neuron	Htr1f, Npy, Rims1, Nxph1, Ptprm, Fgf13, Reln, Ndst3, Lamp5, Slc35d3
Meis2	Meis2+ GABAergic neuron	GABAergic neuron	Igfbpl1, Draxin, Cd1d1, Sp8, Cd24a, Lockd, St8sia2, Gm29260, Gm17750, Meis2
Meis2_Top2a	Meis2+ Top2a+ GABAergic neuron	GABAergic neuron	Igfbpl1, Dcc, E130114P18Rik, Draxin, Cd1d1, Sp8, Ccnd2, Mdk, Meis2, Top2a
Micro	Microglia	microglial cell	Inpp5d, Plxdc2, Tgfbr1, Hexb, Nav2, C1qa, Tanc2, Csmd3, C1qb, Ctss
Oligo Enpp6_1	Enpp6+ oligodendrocyte_1	oligodendrocyte	Pde9a, Inpp5d, Hexb, Panx1, 4932435O22Rik, Tgfbr1, Gm13179, C1qa, Fam114a1, Enpp6
Oligo Enpp6_2	Enpp6+ oligodendrocyte_2	oligodendrocyte	Bmp4, Inpp5d, Hexb, Neu4, 5730559C18Rik, Tgfbr1, Stk32a, C1qa, Ctss, Enpp6
Oligo Enpp6_3	Enpp6+ oligodendrocyte_3	oligodendrocyte	Pde9a, Inpp5d, Hexb, Carmil1, Tgfbr1, Kcnj12, Egflam, C1qa, Gm38039, Enpp6
Oligo Enpp6_4	Enpp6+ oligodendrocyte_4	oligodendrocyte	Gm13883, Plp1, Gm16029, Mbp, Gm26834, St18, Kcnj12, Prr5l, Mobp, Enpp6
Oligo Opalin_1	Opalin+ oligodendrocyte_1	oligodendrocyte	Tmem117, Plp1, Mbp, Enpp6, Tln2, St18, Prr5l, Anln, Selenop, Opalin
Oligo Opalin_2	Opalin+ oligodendrocyte_2	oligodendrocyte	Plp1, Ptgds, Mbp, Il33, St18, C030029H02Rik, Prr5l, Palm2, Mobp, Opalin
Oligo Opalin_3	Opalin+ oligodendrocyte_3	oligodendrocyte	Synpr, Plp1, Mbp, Man1a, St18, Nckap5, Prr5l, Kank1, Pcdh7, Opalin
Oligo Opalin_4	Opalin+ oligodendrocyte_4	oligodendrocyte	Prom1, Plp1, Mbp, Pdzrn3, Thbs3, St18, Cxcl12, Prr5l, Mobp, Opalin
OPC Pdgfra	Pdgfra+ oligodendrocyte precursor cell	oligodendrocyte precursor cell	Plp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Pdgfra
Peri	pericyte	brain pericyte	Plp1, Mbp, St18, Prr5l, Mobp, Mal, Mog, Cldn11, Pde4b, Mag
Pvalb Calb1_1	Pvalb+ Calb1+ GABAergic neuron_1	GABAergic neuron	Plp1, Spp1, Trpc6, Mbp, St18, Gm32647, Npy, Prr5l, Pvalb, Calb1
Pvalb Calb1_2	Pvalb+ Calb1+ GABAergic neuron_2	GABAergic neuron	Lhfpl3, Tac1, Cntnap5c, Vcan, Tnr, Grm7, Ptprz1, Rbp4, Pvalb, Calb1
Pvalb Egfem1	Pvalb+ Egfem1+ GABAergic neuron	GABAergic neuron	Nos1, Atp13a5, 9330158H04Rik, Vtn, Sorcs3, Cald1, Ebf1, Ptprk, Pvalb, Egfem1
Pvalb Gabrg1	Pvalb+ Gabrg1+ GABAergic neuron	GABAergic neuron	Kcnc2, Th, Gabrg1, Erbb4, Gpc4, Sox5, Il1rapl2, Gm16685, Pth2r, Pvalb
Pvalb Gpr149	Pvalb+ Gpr149+ GABAergic neuron	GABAergic neuron	Kcnc2, Fzd6, Mrvi1, Erbb4, Zfpm2, Sox5, Il1rapl2, Dscam, Pvalb, Gpr149
Pvalb Il1rapl2	Pvalb+ Il1rapl2+ GABAergic neuron	GABAergic neuron	Kcnc2, Thsd7a, Pcdh15, Erbb4, Il1rapl2, Sox5, Ncam2, Col25a1, Inpp4b, Pvalb
Pvalb Kank4	Pvalb+ Kank4+ GABAergic neuron	GABAergic neuron	Brinp3, Kcnc2, Erbb4, Sema3e, Lrp1b, Sox5, Il1rapl2, Pcdh9, Pvalb, Kank4
Pvalb Reln	Pvalb+ Reln+ GABAergic neuron	GABAergic neuron	Kcnc2, Cntn5, Erbb4, Reln, Nlgn1, Sox5, Clstn2, Il1rapl2, Gm46102, Pvalb
Pvalb Vipr2_1	Pvalb+ Vipr2+ GABAergic neuron_1	GABAergic neuron	Kcnc2, Crabp1, Prox1, Erbb4, Pcsk6, Sox5, Il1rapl2, Gm37267, Pvalb, Vipr2
Pvalb Vipr2_2	Pvalb+ Vipr2+ GABAergic neuron_2	GABAergic neuron	Unc5b, Kcnc2, Mctp2, Erbb4, Sox5, Pde3a, Il1rapl2, Kit, Pvalb, Vipr2
PVM_1	Perivascular macrophage	perivascular macrophage	F13a1, Kcnc2, Erbb4, Aoah, Ms4a4a, Sox5, Il1rapl2, Colec12, Fam19a2, Gm30489
PVM_2	Perivascular macrophage	perivascular macrophage	Kcnc2, Gm49087, Erbb4, Klra2, H2-Eb1, Sox5, Il1rapl2, H2-Ab1, Fam19a2, 4930562F07Rik
PVM_3	Perivascular macrophage	perivascular macrophage	Napsa, Kcnc2, Erbb4, Slamf7, Gpr141, Sox5, Il1rapl2, H2-Eb1, Fam19a2, H2-Aa
SMC	smooth muscle cell	smooth muscle cell	Acta2, Map3k7cl, Gm6249, Myh11, Tagln, Pdlim3, Ephx3, Olfr558, Crip1, Tbx2
Sncg Calb1_1	Sncg+ Calb1+ GABAergic neuron_1	GABAergic neuron	Cpne5, Adarb2, Cnr1, Ror1, Megf10, Oxr1, Lsamp, Cadps2, Sncg, Calb1
Sncg Calb1_2	Sncg+ Calb1+ GABAergic neuron_2	GABAergic neuron	Tll1, Adarb2, Calb1, Cnr1, Megf10, Cpne5, Stk32a, Cadps2, Gria3, Sncg
Sncg Col14a1	Sncg+ Col14a1+ GABAergic neuron	GABAergic neuron	Luzp2, Adarb2, Cnr1, Cdh6, Megf10, Npy, Cadps2, Erbb4, Sncg, Col14a1
Sncg Npy2r	Sncg+ Npy2r+ GABAergic neuron	GABAergic neuron	Pcdh9, Adarb2, Cnr1, Npy2r, Grik4, Megf10, Cadps2, Kirrel3, Col25a1, Sncg
Sncg Slc17a8	Sncg+ Slc17a8+ GABAergic neuron	GABAergic neuron	Adarb2, Slc17a8, Gas2l3, Cnr1, Nr1h4, Megf10, Adamts18, Cadps2, Kctd12, Sncg
Sst C1ql3_1	Sst+ C1ql3+ GABAergic neuron_1	GABAergic neuron	Adarb2, Pard3bos1, Ptprk, Cnr1, Pard3b, Megf10, Cadps2, Crh, Sst, C1ql3
Sst C1ql3_2	Sst+ C1ql3+ GABAergic neuron_2	GABAergic neuron	Ndnf, Sst, Crh, Grin3a, Nxph1, Pla2g4a, Galntl6, Gm15584, Ntng1, C1ql3
Sst Calb2	Sst+ Calb2+ GABAergic neuron	GABAergic neuron	Sst, Olfm3, Pcsk5, Grin3a, Nkain3, Nxph1, Ptprd, Galntl6, Rgs6, Calb2
Sst Chodl	Sst+ Chodl+ GABAergic neuron	GABAergic neuron	Sst, Grin3a, Nxph1, Galntl6, Rgs6, Sox6, Mgat4c, Synpr, Cacna2d3, Chodl
Sst Crhr2_1	Sst+ Crhr2+ GABAergic neuron_1	GABAergic neuron	Sst, Gm12128, Rspo2, Grin3a, Crtac1, Nxph1, Tmem132d, Galntl6, Alk, Crhr2
Sst Crhr2_2	Sst+ Crhr2+ GABAergic neuron_2	GABAergic neuron	Sst, Grm8, Grin3a, Crybg1, Nxph1, Tmem132b, St6galnac5, Galntl6, Rgs6, Crhr2
Sst Etv1_1	Sst+ Etv1+ GABAergic neuron_1	GABAergic neuron	Fbn2, Sst, C1qtnf7, Grin3a, Nr2f2, Nxph1, Cnih3, Galntl6, Pcdh7, Etv1
Sst Hpse	Sst+ Hpse+ GABAergic neuron	GABAergic neuron	Hpse, Sst, Ust, Grin3a, Nxph1, Syt6, Galntl6, Pdyn, Rgs6, Tox
Sst Htr1a	Sst+ Htr1a+ GABAergic neuron	GABAergic neuron	Sst, Pdyn, Gm30835, Grin3a, Ryr3, Nxph1, Elmo1, Galntl6, Cdh9, Htr1a
Sst Myh8_1	Sst+ Myh8+ GABAergic neuron_1	GABAergic neuron	Plpp4, Sst, Il1rapl2, Grin3a, Nxph1, Cdh12, Chsy3, Galntl6, Rgs6, Myh8
Sst Myh8_2	Sst+ Myh8+ GABAergic neuron_2	GABAergic neuron	Gulp1, Sst, Pld5, Grin3a, Nxph1, Kcnb2, Gas7, Galntl6, Fat3, Myh8
Sst Myh8_3	Sst+ Myh8+ GABAergic neuron_3	GABAergic neuron	Slc24a2, Sst, Cdh9, Grin3a, Nxph1, Elmo1, Galntl6, Npas3, Rgs6, Myh8
Sst Penk	Sst+ Penk+ GABAergic neuron	GABAergic neuron	Sst, Cartpt, Grin3a, Zfp521, Nxph1, 9530026P05Rik, Galntl6, Lama3, Baiap3, Penk
Sst Pvalb Calb2	Sst+ Pvalb+ Calb2+ GABAergic neuron	GABAergic neuron	Moxd1, Sst, Grin3a, Klf12, Kcnab1, Nxph1, Galntl6, Col25a1, Pvalb, Calb2
Sst Pvalb Etv1	Sst+ Pvalb+ Etv1+ GABAergic neuron	GABAergic neuron	Fbn2, Sst, Grin3a, Etv1, Sgcz, Nxph1, Galntl6, Whrn, Rgs6, Pvalb
Sst Tac2	Sst+ Tac2+ GABAergic neuron	GABAergic neuron	Tac2, Sst, Ndnf, Grin3a, Crh, Nxph1, Kcnh8, Galntl6, Myo1b, Rgs6
Sst Th_1	Sst+ Th+ GABAergic neuron_1	GABAergic neuron	Sst, Bcl6, Phactr2, Grin3a, Nxph1, Sorcs3, Galntl6, Antxr2, Serpine2, Th
Sst Th_2	Sst+ Th+ GABAergic neuron_2	GABAergic neuron	Pnoc, Sst, Grin3a, Nr4a2, Nxph1, Th, Rspo3, Galntl6, Rgs6, Gabrg1
Sst Th_3	Sst+ Th+ GABAergic neuron_3	GABAergic neuron	Sst, Corin, Gm36251, Grin3a, Nxph1, Th, Nr4a2, Galntl6, Clec18a, Rgs6
Sst_Pappa	Sst+ Pappa+ GABAergic neuron	GABAergic neuron	Sst, AC129186.1, Grin3a, Layn, Nxph1, Myo5b, Galntl6, Gna14, Rgs6, Pappa
Vip C1ql1	Vip+ C1ql1+ GABAergic neuron	GABAergic neuron	Nos1, Ptprk, A830036E02Rik, Crhbp, Ndst4, Lsamp, Tacr1, Pcdh11x, Vip, C1ql1
Vip Chat_1	Vip+ Chat+ GABAergic neuron_1	GABAergic neuron	Creb5, Vip, Vwc2, Cacna1a, Galnt17, Adarb2, Gpc6, Limch1, Chat, Synpr
Vip Chat_2	Vip+ Chat+ GABAergic neuron_2	GABAergic neuron	Vip, Lypd1, Cacna1a, Kirrel3, Grik4, Adarb2, Limch1, Grm7, Synpr, Chat
Vip Gpc3	Vip+ Gpc3+ GABAergic neuron	GABAergic neuron	Sema6d, Vip, Cacna1a, Lin7a, Alcam, Adarb2, Pcdh11x, Limch1, Synpr, Gpc3
Vip Htr1f_1	Vip+ Htr1f+ GABAergic neuron_1	GABAergic neuron	Cdh6, Vip, Cacna1a, Npy, Mlip, Adarb2, Limch1, Vwc2l, Sntg1, Htr1f
Vip Igfbp6_1	Vip+ Igfbp6+ GABAergic neuron_1	GABAergic neuron	Vip, Stac, Entpd1, Cacna1a, Adarb2, Plcl1, Ptprr, Limch1, Adgrl2, Igfbp6
Vip Igfbp6_2	Vip+ Igfbp6+ GABAergic neuron_2	GABAergic neuron	Reln, Vip, Cacna1a, Cobll1, AC129186.1, Adarb2, Corin, Limch1, Thsd7b, Igfbp6
Vip Mybpc1_1	Vip+ Mybpc1+ GABAergic neuron_1	GABAergic neuron	Vip, Gm45321, Cacna1a, Gm2516, Adarb2, 4930555F03Rik, Limch1, C130073E24Rik, Synpr, Mybpc1
Vip Mybpc1_2	Vip+ Mybpc1+ GABAergic neuron_2	GABAergic neuron	5033421B08Rik, Vip, Cacna1a, Slc7a15, Mybpc1, Adarb2, Limch1, Itih5, Synpr, Col15a1
Vip Mybpc1_3	Vip+ Mybpc1+ GABAergic neuron_3	GABAergic neuron	Grm8, Vip, Cacna1a, Dcc, Grik1, Adarb2, Ryr3, Limch1, Synpr, Mybpc1
Vip Serpinf1_1	Vip+ Serpinf1+ GABAergic neuron_1	GABAergic neuron	Vip, Sfrp2, Cacna1a, Lmo1, Adarb2, Calcrl, Fam196b, Limch1, Dock2, Serpinf1
Vip Serpinf1_2	Vip+ Serpinf1+ GABAergic neuron_2	GABAergic neuron	Vip, Clrn1, Col14a1, Cacna1a, Adarb2, Crtac1, Dpy19l1, Limch1, Gm45680, Serpinf1
Vip Serpinf1_3	Vip+ Serpinf1+ GABAergic neuron_3	GABAergic neuron	Ror1, Vip, Arhgef37, Cacna1a, Adarb2, Drd2, Sv2c, Limch1, Synpr, Serpinf1
Vip Sncg	Sncg+ GABAergic neuron	GABAergic neuron	Vip, Cacna1a, Adra1b, Adarb2, Limch1, Synpr, Cntn4, Sorcs1, Crh, Sncg
VLMC_1	vascular lepotomeningeal cell_1	brain pericyte	Ptgds, Gm30624, Bnc2, Arhgap22, Cped1, Gm47865, Slc7a11, Col15a1, Bmp6, Adgrl3
VLMC_2	vascular lepotomeningeal cell_2	brain pericyte	Aox3, Ptgds, Bnc2, Plxna2, Slc7a11, Cped1, Prex2, Vcam1, Bmp6, Coch
VLMC_3	vascular lepotomeningeal cell_3	brain pericyte	Pkhd1, Ptgds, Rspo2, Bnc2, Cftr, Cped1, Slc7a11, Gm2115, Bmp6, Atp13a5
VLMC_4	vascular lepotomeningeal cell_4	brain pericyte	Ptgds, Sh3gl3, Bnc2, Aifm3, Ppp1r1a, Cped1, Gm27151, Slc7a11, Atp13a5, Bmp6
VLMC_5	vascular lepotomeningeal cell_5	brain pericyte	Slc47a1, Ptgds, Bnc2, Slc4a10, Cped1, Pcdh7, Slc7a11, Tmeff2, Erc2, Bmp6
VLMC_6	vascular lepotomeningeal cell_6	brain pericyte	Ptgds, Prg4, Bnc2, Tspan8, Cped1, Msln, Slc7a11, Dapl1, Bmp6, Fn1
VLMC_7	vascular lepotomeningeal cell_7	brain pericyte	Cubn, Ptgds, Bnc2, Slc7a14, Sptssb, Cped1, Slc7a11, Dapl1, Igfbp3, Bmp6

cross-species cluster

Label	Expanded Label	OBO Ontology ID	Markers
Astro_1	Astrocyte_1	astrocyte	Gfap, Aqp4, Myoc, Pla2g7, Igfbp5, Id4, Mlc1, Ntsr2, Sdc4, Gja1
Astro_2	Astrocyte_2	astrocyte	Slc1a2, Gpc5, Wdr17, Htra1, Slc1a3, Acsl3, Plpp3, Msi2, Dtna, Gabrb1
Chandelier	Chandelier neuron	GABAergic neuron	Pthlh, Pde3a, Mctp2, Kit, Unc5b, Epb41l4a, Mme, 4933432K03Rik, Gm44129, A830036E02Rik
Endo	Endothelial cell	endothelial cell	Flt1, Sgms1, Adgrl4, Slc2a1, Slco1a4, Bsg, Klf2, Ptprg, Sptbn1, Mecom
L2/3 IT	Layer 2-3 glutamatergic neuron, intratelencephalon-projecting	glutamatergic neuron	Celf2, Rgs6, Lingo2, Dab1, Slit3, Lrrtm4, Camk2a, Dscaml1, Cnksr2, 2010300C02Rik
L5 ET_1	Layer 5 glutamatergic neuron, extratelencephalon-projecting_1	glutamatergic neuron	Fam19a1, Cdh13, Gm2164, Kcnt2, Gm19410, Mgat4c, Sgcz, Nav3, Ntng1, Pex5l
L5 ET_2	Layer 5 glutamatergic neuron, extratelencephalon-projecting_2	glutamatergic neuron	Npnt, Vwc2l, Lgr5, Tshz2, Col8a1, Gm26883, Slc26a4, Erg, Trpc7, Gm2164
L5 IT_1	Layer 5 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Ptprd, Lrrc4c, Car10, Brinp3, Celf2, Cux2, R3hdm1, Kcnip4, Fhod3, Kcnh5
L5 IT_2	Layer 5 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Il1rapl2, Iqgap2, AC129186.1, Fras1, Grik3, Scube1, Deptor, Dgkb, A830036E02Rik, Sdk2
L5 IT_3	Layer 5 glutamatergic neuron, intratelencephalon-projecting_3	glutamatergic neuron	Grp, Nxph1, Col12a1, Gm26883, Slit1, Wls, Gm28905, Gpc6, Tshz2, Tox
L5/6 NP	Layer 5-6 glutamatergic neuron, near-projecting	glutamatergic neuron	Olfm3, Kirrel3, Vwc2l, Grik1, Tshz2, Kcnip1, Dcc, Lrrc4c, Gm26883, Adcy2
L6 CT_1	Layer 6 glutamatergic neuron, corticothalamic-projecting_1	glutamatergic neuron	Hs3st4, Shisa6, Gm28928, Sulf2, Cdh18, Bmpr1b, Zfpm2, Nrxn1, Khdrbs3, Foxp2
L6 CT_2	Layer 6 glutamatergic neuron, corticothalamic-projecting_2	glutamatergic neuron	Foxp2, Kctd16, Hs3st4, Ppp3ca, Garnl3, Nrgn, Zfpm2, Edil3, Nos1ap, Khdrbs3
L6 IT_1	Layer 6 glutamatergic neuron, intratelencephalon-projecting_1	glutamatergic neuron	Nell2, Fst, Il1rapl2, Negr1, C1ql3, Brinp3, Satb2, Plcxd3, Bmpr1b, Pou6f2
L6 IT_2	Layer 6 glutamatergic neuron, intratelencephalon-projecting_2	glutamatergic neuron	Ak5, Pcdh7, Nell2, Dcc, Cdh9, Pcsk2, Cplx2, Rasgef1b, Chrm2, C1ql3
L6 IT_3	Layer 6 glutamatergic neuron, intratelencephalon-projecting_3	glutamatergic neuron	Tfap2d, Nr2f2, Oprk1, Gm45623, Smoc2, Gm15825, Car12, 4930555F03Rik, Nr4a2, Lxn
L6b	Layer 6b glutamatergic neuron	glutamatergic neuron	Ctgf, Inpp4b, Cdh18, Tmem163, AC124490.1, Kcnab1, Mmp16, Kcnip4, Erc2, Cplx3
Lamp5_1	Lamp5+ GABAergic neuron_1	GABAergic neuron	Kit, Nxph1, Ndnf, Luzp2, Gm30835, Grin2a, Ndst4, Pde11a, Unc5c, Lamp5
Lamp5_2	Lamp5+ GABAergic neuron_2	GABAergic neuron	Nyap2, Unc5d, Alk, Grin2a, Fgf13, Gad2, Asph, Rims1, Htr1f, Lamp5
Lamp5_3	Lamp5+ GABAergic neuron_3	GABAergic neuron	Dchs2, Lhx6, Nos1, Cntnap3, B020031H02Rik, Gm45680, Ackr3, Tacr1, Cntnap4, Lamp5
Lamp5_4	Lamp5+ GABAergic neuron_4	GABAergic neuron	Col14a1, Luzp2, Pax6, Asph, Frem1, Ralyl, Tnfaip8l3, Dpy19l1, Pnoc, Lamp5
Lamp5_5	Lamp5+ GABAergic neuron_5	GABAergic neuron	Reln, Sorcs1, Cxcl14, Npas3, Rxfp1, Nrg1, Ndst4, Galntl6, Nr2f2, Lamp5
Microglia/PVM	microglia / perivascular macrophage	perivascular macrophage	Inpp5d, Zfhx3, Elmo1, Srgap2, Ccnd3, Tgfbr1, Mef2a, Hexb, Tanc2, Pag1
Oligo_1	oligodendrocyte_1	oligodendrocyte	Prr5l, Tmem117, Plp1, Enpp6, Anln, Tln2, Mobp, St18, Selenop, Mog
Oligo_2	oligodendrocyte_2	oligodendrocyte	Pde4b, Ptgds, Mbp, Erbb4, Plp1, Il33, St18, Kirrel3, Mobp, Nkain2
OPC	oligodendrocyte precursor cell	oligodendrocyte precursor cell	Lhfpl3, Tnr, Vcan, Dscam, Epn2, Xylt1, Ptprz1, Gm4876, Pdgfra, Cacng4
Pvalb_1	Pvalb+ GABAergic neuron_1	GABAergic neuron	Kcnc2, Nrg3, Kcnc1, Gria3, Cntnap4, Cntn5, Btbd11, Gm1604a, Erbb4, Pvalb
Pvalb_2	Pvalb+ GABAergic neuron_2	GABAergic neuron	Shisa8, Corin, Th, 4930509J09Rik, Tac1, Ptprk, Lama3, Nos1, Rbp4, Pvalb
Sncg_1	Sncg+ GABAergic neuron_1	GABAergic neuron	Htr3a, Cntn4, Sp8, Sorcs1, Pnoc, Dpp10, Tnfaip8l3, Ptprd, Frem1, Sncg
Sncg_2	Sncg+ GABAergic neuron_2	GABAergic neuron	Frem1, Col25a1, Npas1, Eps8, Scml4, 9530059O14Rik, Tac2, Malat1, Rgs16, Sncg
Sncg_3	Sncg+ GABAergic neuron_3	GABAergic neuron	Cxcl14, Nell1, Rgs12, Spock1, Npas1, Ppp2r2b, Igf1, Pcdh9, Megf10, Sncg
Sncg_4	Sncg+ GABAergic neuron_4	GABAergic neuron	Egln3, Nrxn3, Col14a1, Cntnap5b, Tnfaip8l3, Itga8, Rxfp1, Fam19a1, Npas1, Sncg
Sst Chodl	Sst+ Chodl+ GABAergic neuron	GABAergic neuron	Nos1, Crhbp, Ndst4, Tacr1, Chodl, 9330158H04Rik, Fndc1, Stac, Bace2, Sst
Sst_1	Sst+ GABAergic neuron_1	GABAergic neuron	Pdyn, Cdh9, Npas1, Cntnap2, AF529169, Ano3, Reln, Zfp804a, Lhx6, Sst
Sst_2	Sst+ GABAergic neuron_2	GABAergic neuron	Il1rapl2, Nebl, Sst, Pcdh7, Reln, Gabrb1, Rab3b, Kctd8, Cntn6, Sst
Sst_3	Sst+ GABAergic neuron_3	GABAergic neuron	Gria1, Gpc6, Etl4, Sst, Adgrb3, Grin3a, Pcdh9, Xkr4, Sh3rf3, Sst
Sst_4	Sst+ GABAergic neuron_4	GABAergic neuron	Npas1, Unc5d, 9630002D21Rik, Cdh9, Lhx6, Egfem1, Lypd6, Pou6f2, Sytl5, Sst
Sst_5	Sst+ GABAergic neuron_5	GABAergic neuron	9630002D21Rik, Adgrb3, Crh, Gm20754, Npas1, Kcnc2, Gxylt2, Pard3b, Pard3bos1, Sst
Sst_6	Sst+ GABAergic neuron_6	GABAergic neuron	9630002D21Rik, B3galt1, Crh, Reln, Klhl14, Ptprm, Npas1, Grm1, Gxylt2, Sst
Sst_7	Sst+ GABAergic neuron_7	GABAergic neuron	Th, Cdh9, Corin, Lingo2, Cort, Ncam2, Nxph2, Arpp21, Gm36251, Sst
Vip_1	Vip+ GABAergic neuron_1	GABAergic neuron	Vip, Cntnap2, Zfp804a, Kcnip4, Sobp, Gpc6, Sdk1, Brinp3, Sorcs3, Fstl5
Vip_2	Vip+ GABAergic neuron_2	GABAergic neuron	Vip, Cxcl14, Adarb2, Clstn2, Synpr, Oxr1, Igf1, Fam19a2, Shisa9, Crh
Vip_3	Vip+ GABAergic neuron_3	GABAergic neuron	Vip, Alcam, Igf1, Astn2, Prox1, Pde3a, Grpr, Lin7a, Crh, Pthlh
Vip_4	Vip+ GABAergic neuron_4	GABAergic neuron	Penk, Thsd7a, Gm39185, Nrg3, Npas1, Ccser1, Crh, Thsd7b, Stac, Calb2
VLMC	vascular lepotomeningeal cell	brain pericyte	Cped1, Apod, Ptgds, Atp1a2, Slc6a20a, Colec12, Bmp6, Ranbp3l, Slc7a11, Lama1