neuron_markers.txt

# Neurons

>Inhibitory
expressed: GAD1, GAD2, SOX6, PVALB, SST, VIP, LHX6, NDNF, CALB2, SULF1
not expressed: SLC17A7, SATB2

>Excitatory
expressed: SLC17A7, SATB2, RORB, CUX2, TLE4, NR4A2, SEMA3C
not expressed: GAD1, GAD2, SOX6, PVALB

# Inhibitory

>Id2
expressed: ID2, LAMP5, CALB2, PAX6, RELN, SV2C, COL5A2, SEMA3C, FAM19A1, SPOCK1, MYO5B
not expressed: VIP, TAC3, FAM89A, NPR3, SST, LHX6
subtype of: Inhibitory

>Pvalb
expressed: PVALB, NOS1, SULF1, LHX6, KCNS3, CRH, PLEKHH2, LGR5
not expressed: LAMP5, ID2, SST, FAM89A, RELN, SEMA6A, TAC3, DDR2, VIP
subtype of: Inhibitory

>Sst
expressed: SST, NOS1, SEMA6A, FAM89A, LHX6, GRIK1
not expressed: VIP, CALB2, CRH, CHAT, CCK, LAMP5, ID2, SV2C, PDGFD, PVALB, KCNS3, ADORB1
subtype of: Inhibitory

>Vip
expressed: VIP, TAC3, CALB2, LAMA3, FAM19A1, NPR3
not expressed: NOS1, LAMP5, PDGFD, SV2C, LHX6, NXPH1, ID2
subtype of: Inhibitory

## Id2

>Id2_Lamp5
expressed: LAMP5, PDGFD, SV2C
not expressed: PAX6, CALB2
subtype of: Id2

>Id2_Nckap5
expressed: CALB2, SYNPR, NCKAP5
not expressed: LAMP5, SV2C, PAX6
subtype of: Id2

>Id2_Pax6
expressed: PAX6, NXPH1, GRIN2A
not expressed: LAMP5, SV2C
subtype of: Id2

### Id2_Lamp5

>Id2_Lamp5_Nos1
expressed: NOS1, SFRP1, LHX6, SULF1
not expressed: LAMA3
subtype of: Id2_Lamp5

>Id2_Lamp5_Crh
expressed: CRH, SFRP1, ID2, LAMA3
not expressed: LHX6, SULF1
subtype of: Id2_Lamp5

>Id2_Lamp5_Nmbr
expressed: RELN, LAMA3
not expressed: ID2
subtype of: Id2_Lamp5

## Pvalb

>Pvalb_Nos1
expressed: NOS1, CALB1 # LHX6
not expressed: CRH, NOG, UNC5B, NPNT #, CA8
subtype of: Pvalb

>Pvalb_Sulf1
expressed: SULF1, MEPE # LHX6, CPED1
not expressed: CRH, NOG, UNC5B, NPNT, NOS1, CALB1, LGR5
subtype of: Pvalb

>Pvalb_Lgr5
expressed: LGR5, MEPE # LHX6, CPED1
not expressed: CRH, NOG, UNC5B, NPNT, NOS1, CALB1, SULF1
subtype of: Pvalb

>Pvalb_Crh
expressed: CRH, NOG, UNC5B, NPNT # PLEKHH2, CA8
not expressed: NOS1, CALB1 #, RGS5, LHX6
subtype of: Pvalb

## Sst

>Sst_Th
expressed uniq: TH
expressed: GABRG3 # FBN2
not expressed: TAC3, THSD7B, CALB1, HPGD, TAC1
subtype of: Sst

>Sst_Tac3
expressed: TAC3, GABRG3, RELN
not expressed: TH, STK32A, HPGD, SCGZ
subtype of: Sst

>Sst_Tac1
expressed uniq: TAC1
expressed: TAC3, GABRG3
not expressed: RELN, TH, FBN2, CALB1, GXYLT2, NOS1
subtype of: Sst

>Sst_Stk32a
expressed: STK32A, RELN, GXYLT2
not expressed: TH, TAC3, FBN2, HPGD
subtype of: Sst

>Sst_Nos1
expressed: GXYLT2, FBN2, CALB1, NOS1
not expressed: TH, TAC3, HPGD, SGCZ, GABRG3
subtype of: Sst

>Sst_Calb1
expressed: HPGD, CALB1, FBN2
not expressed: TAC3, TH, GXYLT2, ADGRG6
subtype of: Sst

>Sst_Isoc1
expressed uniq: THSD7B
expressed: SGCD, GABRG3
not expressed: RELN, SOX6
subtype of: Sst

## Vip

>Vip_Abi3bp
expressed uniq: ABI3BP
expressed: GRM1
not expressed: ZMAT4
subtype of: Vip

>Vip_Tyr
expressed: TOX2, LUZP2, TYR
not expressed: ZMAT4, HTR2C
subtype of: Vip

>Vip_Crh
expressed: CRH
not expressed: SEMA3C, SEMA6A, HTR2C, TOX2
subtype of: Vip

>Vip_Sstr1
expressed: TRPM3, SSTR1
# expressed: PLCXD3, MAML3
# not expressed: RELN, ZNF804A, ADAM33
not expressed: CRH, NRG1
subtype of: Vip

>Vip_Sema3c
expressed: THSD7B, PENK, SEMA3C, ADAMTSL1
not expressed: KCNQ5, CRH, RELN, ADAM33, PTPRK
# not expressed: ZMAT4
subtype of: Vip

>Vip_Nrg1
expressed: NRG1, GGH, SGCZ
not expressed: KCNQ5, PENK, CRH, CNTN5
subtype of: Vip

>Vip_Cbln1
expressed: HTR2C, CBLN1
not expressed: FSTL5, PENK
subtype of: Vip

# Excitatory

>L2_3_Cux2
expressed uniq: LAMP5, LAMA2
expressed: CUX2, PDGFD, FREM3, COL5A2
not expressed: GABRG1, TLL1, GRIN3A
subtype of: Excitatory

>L4_Rorb
expressed uniq: MME
expressed: RORB, COBLL1, SCHLAP1, PLCH1
not expressed: PDGFD, PXDN, OPRK1, COL5A2
subtype of: Excitatory

>L5_6_Themis
expressed: THEMIS, NR4A2, PXDN, OPRK1
not expressed: CUX2, RORB
subtype of: Excitatory

>L5_6_Fezf2
expressed uniq: CMTM8, FEZF2
expressed: TLE4, LRRK1, ADRA1A, RORB
not expressed: CUX2, SCHLAP1, COBLL1
subtype of: Excitatory

## L2_3_Cux2

>L2_Cux2_Lamp5
expressed: LAMP5, PARD3, PDGFD, LTK, DCC
not expressed: COBLL1, PLCH1, RORB, GABRG1, COL5A2, NTNG1, FREM3, LAMA2, GLIS3
subtype of: L2_3_Cux2

>L2_3_Cux2_Frem3
expressed: FREM3, AGBL1, GPC6, LAMA2, GLIS3
not expressed: PRSS12, COBLL1, PLCH1, RORB, DCC, LAMP5, PARD3, PDGFD, LTK, COL5A2, CCBE1
subtype of: L2_3_Cux2

>L3_Cux2_Prss12
expressed: PRSS12, COBLL1, PLCH1, RORB, DCC, LAMA2, COL5A2
not expressed: LAMP5, PARD3, PDGFD
subtype of: L2_3_Cux2

# ### L2_Cux2_Lamp5
# 
# >L2_Cux2_Lamp5_Pdgfd
# expressed: PDGFD, DCC, ACVR1C
# not expressed: FREM3
# subtype of: L2_Cux2_Lamp5
# 
# >L2_Cux2_Lamp5_March1
# expressed: MARCH1, FREM3, PARD3, CCBE
# not expressed: PDGFD, DCC
# subtype of: L2_Cux2_Lamp5

## L4_Rorb

>L4_Rorb_Mme
expressed: MME, PLCH1, COL22A1
not expressed: ARHGAP15, GABRG1, MET, TPBG
subtype of: L4_Rorb

>L4_Rorb_Met
expressed: MET, GABRG1, TPBG, COBLL1
not expressed: ARHGAP15, COL22A1, TLL1
subtype of: L4_Rorb

>L4_Rorb_Arhgap15
expressed: ARHGAP15, ADGRL4, TLL1, TPBG
not expressed: MME, MET
subtype of: L4_Rorb

## L5_6_Themis

>L5_6_Themis_Sema3a
expressed: SEMA3A, PXDN, GRIK3
not expressed: NR4A2, DCSTAMP, NTNG2
subtype of: L5_6_Themis

>L5_6_Themis_Ntng2
expressed: NR4A2, DCSTAMP, NTNG2
not expressed: SEMA3A, PXDN, GRIK3
subtype of: L5_6_Themis

## L5_6_Fezf2

> L5_6_Fezf2_Lrrk1
expressed: LRRK1, ARSJ, CAMK2D
not expressed: TLE4, SEMA5A, HTR2C
subtype of: L5_6_Fezf2

> L5_6_Fezf2_Tle4
expressed: TLE4, SEMA3A, HTR2C, SEMA5A
not expressed: LRRK1
subtype of: L5_6_Fezf2

### L5_6_Fezf2_Tle4

> L5_6_Fezf2_Tle4_Abo
expressed: ABO, SEMA5A
not expressed: HTR2C
subtype of: L5_6_Fezf2_Tle4

> L5_6_Fezf2_Tle4_Htr2c
expressed: HTR2C, IL26, CARD11, KCNIP1
not expressed: ABO, SCUBE1
subtype of: L5_6_Fezf2_Tle4

> L5_6_Fezf2_Tle4_Scube1
expressed: SCUBE1, NR4A2, CDH10, SLC15A5
not expressed: ABO, HTR2C, SEMA5A
subtype of: L5_6_Fezf2_Tle4

### L5_6_Fezf2_Lrrk1

> L5_6_Fezf2_Lrrk1_Pcp4
expressed: PCP4, SLIT3
not expressed: SEMA3E, TSHZ2
subtype of: L5_6_Fezf2_Lrrk1

> L5_6_Fezf2_Lrrk1_Sema3e
expressed: SEMA3E, TSHZ2
not expressed: PCP4, SLIT3
subtype of: L5_6_Fezf2_Lrrk1