analysis/01.SelectGenes/Markers_1.2/comparison_CellTypes-Markers_1.1-Markers_1.2.md
In oganm/brainGenesManuscript: Marker genes of brain cell types and their use in analysis of whole tissue data
All
Astrocyte
Total gene count: 97
removed (3): Cyr61, Sox9, Vegfa
added (3): Ccn1, Gpam, Pdgfc
Ependymal
Total gene count: 45
removed (1): D930015E06Rik
added (1): Tmem131l
Microglia
Total gene count: 136
added (5): Clic1, Otulinl, Sqor, Srgap2, Tcim
Microglia_activation
Total gene count: 96
removed (2): Igtp, Sqrdl
added (2): Gbp7, Slc39a8
Microglia_deactivation
Total gene count: 104
removed (5): 1810011O10Rik, Fam105a, Prkcd, Samhd1, St3gal6
Noradrenergic
Total gene count: 12
added (3): Gstm6, Pmfbp1, Stbd1
Oligo
Total gene count: 23
removed (1): Mobp
added (1): Lpar1
Purkinje
Total gene count: 27
added (1): Lhx1
Amygdala
Astrocyte
Total gene count: 150
removed (3): Cyr61, Sorcs2, Vegfa
added (3): Adgrg1, Ccn1, Gpam
Microglia
Total gene count: 151
removed (1): Skap2
added (2): Otulinl, Sqor
Microglia_activation
Total gene count: 101
removed (1): Sqrdl
Microglia_deactivation
Total gene count: 143
removed (4): Cd2ap, Fam105a, Man2b1, Tmcc3
added (1): Scamp2
Pyramidal
Total gene count: 22
added (1): Bdnf
BasalForebrain
Astrocyte
Total gene count: 149
removed (3): Cyr61, Notch1, Sox9
added (3): Add3, Ccn1, Gpam
ForebrainCholin
Total gene count: 91
removed (3): Chd3os, Hs6st2, Nipsnap1
added (1): Rnf227
Microglia
Total gene count: 159
added (3): Gns, Otulinl, Resf1
Microglia_deactivation
Total gene count: 133
removed (3): 2810474O19Rik, Fam105a, St3gal6
Brainstem
Astrocyte
Total gene count: 141
removed (2): Cyr61, Sox21
added (4): Aqp4, Ccn1, Gpam, Pdk4
BrainstemCholin
Total gene count: 30
added (1): Hspb8
Microglia
Total gene count: 154
removed (2): Adamts1, Dusp6
added (2): Otulinl, Resf1
Microglia_activation
Total gene count: 108
added (1): Il4ra
Microglia_deactivation
Total gene count: 138
removed (4): 2810474O19Rik, Fam105a, Fosb, St3gal6
Noradrenergic
Total gene count: 16
removed (1): Gstm6
Oligo
Total gene count: 24
removed (1): Josd2
Cerebellum
Basket
Total gene count: 8
added (1): Cidea
CerebGranule
Total gene count: 6
added (1): Calb2
Golgi
Total gene count: 27
removed (1): Resp18
Microglia
Total gene count: 191
removed (3): Apobec1, Diaph2, Ssfa2
added (5): Itprid2, Otulinl, Resf1, Sqor, Tcim
Microglia_activation
Total gene count: 125
removed (2): Cd164, Sqrdl
Microglia_deactivation
Total gene count: 159
removed (4): 1810011O10Rik, 2810474O19Rik, Fam105a, St3gal6
Oligo
Total gene count: 50
removed (1): Mobp
Cerebrum
Astrocyte
Total gene count: 178
removed (1): Cyr61
added (3): Ccn1, Cyp2j6, Gpam
ForebrainCholin
Total gene count: 21
removed (1): Gpx3
GabaPV
Total gene count: 6
added (1): Syt2
Gluta
Total gene count: 2
added (1): Lypd1
Microglia
Total gene count: 178
added (4): Ctsz, Otulinl, Sqor, Tcim
Microglia_activation
Total gene count: 122
removed (1): Sqrdl
added (1): Gbp7
Microglia_deactivation
Total gene count: 145
removed (3): 1810011O10Rik, Fam105a, St3gal6
Oligo
Total gene count: 46
removed (2): Mobp, Thbs3
Cortex
Astrocyte
Total gene count: 304
removed (7): 1700040N02Rik, 1700084C01Rik, 2010110P09Rik, 2210417K05Rik, 5033411D12Rik, Ccdc37, Rorb
added (9): Bcas1os2, Ccdc190, Cfap100, Chp2, Hk1os, Sugct, 2810459M11Rik, Gpam, Ccn1
Endothelial
Total gene count: 191
removed (8): 1810011O10Rik, 5430416O09Rik, 8430408G22Rik, Ccdc109b, Gatsl3, Mfsd7c, Ptrf, Sdpr
added (8): Castor1, Cavin1, Cavin2, Depp1, Flvcr2, Mcub, Spaar, Tcim
GabaPV
Total gene count: 27
added (1): Gpr83
GabaRelnCalb
Total gene count: 23
removed (1): Gm889
added (1): Lsmem1
GabaVIPReln
Total gene count: 48
removed (2): 2310042E22Rik, Mir374
added (3): Teddm3, Mir374b, Slc44a5
Microglia
Total gene count: 294
removed (8): Tmem8c, 1700011I03Rik, 1810011H11Rik, 6530439I21, A430071A18Rik, Gm4902, Gm8348, Rasl2-9-ps
added (13): C5ar2, Ccdc192, Gm10409, Gm15850, Lilr4b, Mymk, Otulinl, Phf11b, Rptoros, Rubcnl, Tent5c, Tmem273, Sqor
Microglia_activation
Total gene count: 120
removed (4): 5031414D18Rik, Gp49a, Gpr77, Sqrdl
Microglia_deactivation
Total gene count: 206
removed (3): Fam105a, Fam46c, St3gal6
added (3): Ndst2, Rasl2-9, Siglec5
Oligo
Total gene count: 165
removed (6): Fbxo36, 4933413G19Rik, 9330117O12, Gm505, Hn1l, Speer7-ps1
added (7): Fign, 9330117O12Rik, Jpt2, Speer4cos, Sprtn, Stxbp3a, Tex52
OligoPrecursors
Total gene count: 211
removed (7): 3632451O06Rik, 9930021D14Rik, Gm10391, Gm10394, Murc, Tmem146, Zcchc16
added (7): Armh4, Bricd5, Catsperd, Cavin4, Duxbl2, Duxbl3, Rtl4
Pyramidal
Total gene count: 39
added (4): Dnajb5, Pcsk2, Syt16, Zfyve28
Hippocampus
Astrocyte
Total gene count: 141
removed (2): Cyr61, Sox9
added (5): Agl, Ccn1, Cspg5, Dtna, Gpam
GabaSSTReln
Total gene count: 53
removed (2): Entpd4, Pcsk1
Microglia
Total gene count: 157
added (3): Gns, Otulinl, Sqor
Microglia_activation
Total gene count: 111
removed (1): Sqrdl
added (1): Atp7a
Microglia_deactivation
Total gene count: 135
removed (2): Fam105a, St3gal6
Oligo
Total gene count: 49
removed (1): Mobp
added (1): Tnni1
Pyramidal
Total gene count: 17
removed (1): Nov
added (1): Ccn3
LocusCoeruleus
Astrocyte
Total gene count: 143
removed (1): Cyr61
added (5): Acaa2, Ccn1, Gpam, Notch1, Sox9
Microglia
Total gene count: 149
removed (1): Myo1b
added (1): Otulinl
Microglia_activation
Total gene count: 106
added (1): Plaur
Microglia_deactivation
Total gene count: 137
removed (2): Fam105a, St3gal6
Noradrenergic
Total gene count: 136
added (2): Dmtn, Dync1i1
Oligo
Total gene count: 55
added (2): E330009J07Rik, Tmeff2
Midbrain
Astrocyte
Total gene count: 128
removed (3): Crot, Cyr61, Tmem51
added (3): Bcan, Ccn1, Gpam
BrainstemCholin
Total gene count: 36
added (1): Syt2
Microglia
Total gene count: 156
added (3): Otulinl, Resf1, Tgif2
Microglia_deactivation
Total gene count: 134
removed (4): 2810474O19Rik, Fam105a, Slc7a8, St3gal6
Oligo
Total gene count: 18
removed (1): Aspa
SpinalCord
Astrocyte
Total gene count: 140
removed (2): Cyr61, Itsn1
added (2): Ccn1, Gpam
Microglia
Total gene count: 150
removed (1): Emp3
added (2): Otulinl, Resf1
Microglia_activation
Total gene count: 104
added (1): Atp7a
Microglia_deactivation
Total gene count: 132
removed (4): 2810474O19Rik, Fam105a, Lst1, St3gal6
SpinalCordCholinergic
Total gene count: 128
removed (1): Chd3os
added (3): Rnf227, Syt2, Timm10b
Striatum
Astrocyte
Total gene count: 196
removed (1): Cyr61
added (4): Ccn1, Gpam, Lrp4, Metrn
ForebrainCholin
Total gene count: 43
removed (2): Stmn2, Unc119
Microglia
Total gene count: 174
added (6): Cklf, Otulinl, Resf1, Rin2, Spata13, Tcim
Microglia_activation
Total gene count: 115
added (1): Gbp7
Microglia_deactivation
Total gene count: 143
removed (3): 1810011O10Rik, 2810474O19Rik, Fam105a
Oligo
Total gene count: 54
added (2): Cdc42ep1, Ninj2
Spiny
Total gene count: 73
added (1): Cap2
Subependymal
Astrocyte
Total gene count: 113
removed (1): Cyr61
added (2): Ccn1, Emp2
Ependymal
Total gene count: 47
removed (2): D930015E06Rik, Top2a
added (1): Tmem131l
Microglia
Total gene count: 114
removed (1): B2m
added (1): Otulinl
Microglia_deactivation
Total gene count: 103
removed (2): Fam105a, St3gal6
added (3): Lst1, Naip6, Pycard
Oligo
Total gene count: 53
removed (1): Mobp
added (1): Wfdc18
SubstantiaNigra
Astrocyte
Total gene count: 97
removed (3): Axl, Cyr61, Rorb
added (4): Add3, Ccn1, Notch1, Trps1
Dopaminergic
Total gene count: 58
removed (2): Cers4, Epb41l1
added (2): Gria3, Syp
Microglia
Total gene count: 147
added (2): B2m, Otulinl
Microglia_activation
Total gene count: 94
removed (1): Tlr6
Microglia_deactivation
Total gene count: 127
removed (2): Fam105a, St3gal6
added (1): Lst1
Oligo
Total gene count: 17
removed (1): Tspan2
Thalamus
Astrocyte
Total gene count: 161
removed (2): Cyr61, Fbln1
added (3): Ccn1, Gpam, Sox9
Microglia
Total gene count: 159
removed (1): Cklf
added (2): Otulinl, Resf1
Microglia_deactivation
Total gene count: 136
removed (3): 2810474O19Rik, Fam105a, St3gal6
added (2): Naip6, Rbl1
Oligo
Total gene count: 34
removed (1): Mobp
oganm/brainGenesManuscript documentation built on Aug. 24, 2022, 7:48 p.m.
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All
Astrocyte
Total gene count: 97
removed (3): Cyr61, Sox9, Vegfa
added (3): Ccn1, Gpam, Pdgfc
Ependymal
Total gene count: 45
removed (1): D930015E06Rik
added (1): Tmem131l
Microglia
Total gene count: 136
added (5): Clic1, Otulinl, Sqor, Srgap2, Tcim
Microglia_activation
Total gene count: 96
removed (2): Igtp, Sqrdl
added (2): Gbp7, Slc39a8
Microglia_deactivation
Total gene count: 104
removed (5): 1810011O10Rik, Fam105a, Prkcd, Samhd1, St3gal6
Noradrenergic
Total gene count: 12
added (3): Gstm6, Pmfbp1, Stbd1
Oligo
Total gene count: 23
removed (1): Mobp
added (1): Lpar1
Purkinje
Total gene count: 27
added (1): Lhx1
Amygdala
Astrocyte
Total gene count: 150
removed (3): Cyr61, Sorcs2, Vegfa
added (3): Adgrg1, Ccn1, Gpam
Microglia
Total gene count: 151
removed (1): Skap2
added (2): Otulinl, Sqor
Microglia_activation
Total gene count: 101
removed (1): Sqrdl
Microglia_deactivation
Total gene count: 143
removed (4): Cd2ap, Fam105a, Man2b1, Tmcc3
added (1): Scamp2
Pyramidal
Total gene count: 22
added (1): Bdnf
BasalForebrain
Astrocyte
Total gene count: 149
removed (3): Cyr61, Notch1, Sox9
added (3): Add3, Ccn1, Gpam
ForebrainCholin
Total gene count: 91
removed (3): Chd3os, Hs6st2, Nipsnap1
added (1): Rnf227
Microglia
Total gene count: 159
added (3): Gns, Otulinl, Resf1
Microglia_deactivation
Total gene count: 133
removed (3): 2810474O19Rik, Fam105a, St3gal6
Brainstem
Astrocyte
Total gene count: 141
removed (2): Cyr61, Sox21
added (4): Aqp4, Ccn1, Gpam, Pdk4
BrainstemCholin
Total gene count: 30
added (1): Hspb8
Microglia
Total gene count: 154
removed (2): Adamts1, Dusp6
added (2): Otulinl, Resf1
Microglia_activation
Total gene count: 108
added (1): Il4ra
Microglia_deactivation
Total gene count: 138
removed (4): 2810474O19Rik, Fam105a, Fosb, St3gal6
Noradrenergic
Total gene count: 16
removed (1): Gstm6
Oligo
Total gene count: 24
removed (1): Josd2
Cerebellum
Basket
Total gene count: 8
added (1): Cidea
CerebGranule
Total gene count: 6
added (1): Calb2
Golgi
Total gene count: 27
removed (1): Resp18
Microglia
Total gene count: 191
removed (3): Apobec1, Diaph2, Ssfa2
added (5): Itprid2, Otulinl, Resf1, Sqor, Tcim
Microglia_activation
Total gene count: 125
removed (2): Cd164, Sqrdl
Microglia_deactivation
Total gene count: 159
removed (4): 1810011O10Rik, 2810474O19Rik, Fam105a, St3gal6
Oligo
Total gene count: 50
removed (1): Mobp
Cerebrum
Astrocyte
Total gene count: 178
removed (1): Cyr61
added (3): Ccn1, Cyp2j6, Gpam
ForebrainCholin
Total gene count: 21
removed (1): Gpx3
GabaPV
Total gene count: 6
added (1): Syt2
Gluta
Total gene count: 2
added (1): Lypd1
Microglia
Total gene count: 178
added (4): Ctsz, Otulinl, Sqor, Tcim
Microglia_activation
Total gene count: 122
removed (1): Sqrdl
added (1): Gbp7
Microglia_deactivation
Total gene count: 145
removed (3): 1810011O10Rik, Fam105a, St3gal6
Oligo
Total gene count: 46
removed (2): Mobp, Thbs3
Cortex
Astrocyte
Total gene count: 304
removed (7): 1700040N02Rik, 1700084C01Rik, 2010110P09Rik, 2210417K05Rik, 5033411D12Rik, Ccdc37, Rorb
added (9): Bcas1os2, Ccdc190, Cfap100, Chp2, Hk1os, Sugct, 2810459M11Rik, Gpam, Ccn1
Endothelial
Total gene count: 191
removed (8): 1810011O10Rik, 5430416O09Rik, 8430408G22Rik, Ccdc109b, Gatsl3, Mfsd7c, Ptrf, Sdpr
added (8): Castor1, Cavin1, Cavin2, Depp1, Flvcr2, Mcub, Spaar, Tcim
GabaPV
Total gene count: 27
added (1): Gpr83
GabaRelnCalb
Total gene count: 23
removed (1): Gm889
added (1): Lsmem1
GabaVIPReln
Total gene count: 48
removed (2): 2310042E22Rik, Mir374
added (3): Teddm3, Mir374b, Slc44a5
Microglia
Total gene count: 294
removed (8): Tmem8c, 1700011I03Rik, 1810011H11Rik, 6530439I21, A430071A18Rik, Gm4902, Gm8348, Rasl2-9-ps
added (13): C5ar2, Ccdc192, Gm10409, Gm15850, Lilr4b, Mymk, Otulinl, Phf11b, Rptoros, Rubcnl, Tent5c, Tmem273, Sqor
Microglia_activation
Total gene count: 120
removed (4): 5031414D18Rik, Gp49a, Gpr77, Sqrdl
Microglia_deactivation
Total gene count: 206
removed (3): Fam105a, Fam46c, St3gal6
added (3): Ndst2, Rasl2-9, Siglec5
Oligo
Total gene count: 165
removed (6): Fbxo36, 4933413G19Rik, 9330117O12, Gm505, Hn1l, Speer7-ps1
added (7): Fign, 9330117O12Rik, Jpt2, Speer4cos, Sprtn, Stxbp3a, Tex52
OligoPrecursors
Total gene count: 211
removed (7): 3632451O06Rik, 9930021D14Rik, Gm10391, Gm10394, Murc, Tmem146, Zcchc16
added (7): Armh4, Bricd5, Catsperd, Cavin4, Duxbl2, Duxbl3, Rtl4
Pyramidal
Total gene count: 39
added (4): Dnajb5, Pcsk2, Syt16, Zfyve28
Hippocampus
Astrocyte
Total gene count: 141
removed (2): Cyr61, Sox9
added (5): Agl, Ccn1, Cspg5, Dtna, Gpam
GabaSSTReln
Total gene count: 53
removed (2): Entpd4, Pcsk1
Microglia
Total gene count: 157
added (3): Gns, Otulinl, Sqor
Microglia_activation
Total gene count: 111
removed (1): Sqrdl
added (1): Atp7a
Microglia_deactivation
Total gene count: 135
removed (2): Fam105a, St3gal6
Oligo
Total gene count: 49
removed (1): Mobp
added (1): Tnni1
Pyramidal
Total gene count: 17
removed (1): Nov
added (1): Ccn3
LocusCoeruleus
Astrocyte
Total gene count: 143
removed (1): Cyr61
added (5): Acaa2, Ccn1, Gpam, Notch1, Sox9
Microglia
Total gene count: 149
removed (1): Myo1b
added (1): Otulinl
Microglia_activation
Total gene count: 106
added (1): Plaur
Microglia_deactivation
Total gene count: 137
removed (2): Fam105a, St3gal6
Noradrenergic
Total gene count: 136
added (2): Dmtn, Dync1i1
Oligo
Total gene count: 55
added (2): E330009J07Rik, Tmeff2
Midbrain
Astrocyte
Total gene count: 128
removed (3): Crot, Cyr61, Tmem51
added (3): Bcan, Ccn1, Gpam
BrainstemCholin
Total gene count: 36
added (1): Syt2
Microglia
Total gene count: 156
added (3): Otulinl, Resf1, Tgif2
Microglia_deactivation
Total gene count: 134
removed (4): 2810474O19Rik, Fam105a, Slc7a8, St3gal6
Oligo
Total gene count: 18
removed (1): Aspa
SpinalCord
Astrocyte
Total gene count: 140
removed (2): Cyr61, Itsn1
added (2): Ccn1, Gpam
Microglia
Total gene count: 150
removed (1): Emp3
added (2): Otulinl, Resf1
Microglia_activation
Total gene count: 104
added (1): Atp7a
Microglia_deactivation
Total gene count: 132
removed (4): 2810474O19Rik, Fam105a, Lst1, St3gal6
SpinalCordCholinergic
Total gene count: 128
removed (1): Chd3os
added (3): Rnf227, Syt2, Timm10b
Striatum
Astrocyte
Total gene count: 196
removed (1): Cyr61
added (4): Ccn1, Gpam, Lrp4, Metrn
ForebrainCholin
Total gene count: 43
removed (2): Stmn2, Unc119
Microglia
Total gene count: 174
added (6): Cklf, Otulinl, Resf1, Rin2, Spata13, Tcim
Microglia_activation
Total gene count: 115
added (1): Gbp7
Microglia_deactivation
Total gene count: 143
removed (3): 1810011O10Rik, 2810474O19Rik, Fam105a
Oligo
Total gene count: 54
added (2): Cdc42ep1, Ninj2
Spiny
Total gene count: 73
added (1): Cap2
Subependymal
Astrocyte
Total gene count: 113
removed (1): Cyr61
added (2): Ccn1, Emp2
Ependymal
Total gene count: 47
removed (2): D930015E06Rik, Top2a
added (1): Tmem131l
Microglia
Total gene count: 114
removed (1): B2m
added (1): Otulinl
Microglia_deactivation
Total gene count: 103
removed (2): Fam105a, St3gal6
added (3): Lst1, Naip6, Pycard
Oligo
Total gene count: 53
removed (1): Mobp
added (1): Wfdc18
SubstantiaNigra
Astrocyte
Total gene count: 97
removed (3): Axl, Cyr61, Rorb
added (4): Add3, Ccn1, Notch1, Trps1
Dopaminergic
Total gene count: 58
removed (2): Cers4, Epb41l1
added (2): Gria3, Syp
Microglia
Total gene count: 147
added (2): B2m, Otulinl
Microglia_activation
Total gene count: 94
removed (1): Tlr6
Microglia_deactivation
Total gene count: 127
removed (2): Fam105a, St3gal6
added (1): Lst1
Oligo
Total gene count: 17
removed (1): Tspan2
Thalamus
Astrocyte
Total gene count: 161
removed (2): Cyr61, Fbln1
added (3): Ccn1, Gpam, Sox9
Microglia
Total gene count: 159
removed (1): Cklf
added (2): Otulinl, Resf1
Microglia_deactivation
Total gene count: 136
removed (3): 2810474O19Rik, Fam105a, St3gal6
added (2): Naip6, Rbl1
Oligo
Total gene count: 34
removed (1): Mobp
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