Neonatal whole brain: Rosenberg et al 2018

Search the single-cell neonatal mouse brain dataset by Rosenberg et al

More information on methods here

Bokeh Plot

Heatmap units: mean log2(counts per 10,000 + 1)

Original study website: N/A

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Metacell IDCluster NameClassMarker Genes from LiteratureNumber Cells
1 OB Mitral/Tufted EomesOlfactory Bulb Mitral and Tufted – EomesNeuron olfactory bulbTbx21117
2 OB Mitral/Tufted Ms4a15Olfactory Bulb Mitral and Tufted – Ms4a15Neuron olfactory bulbTbx21271
3 OB Mitral/Tufted SvilOlfactory Bulb Mitral and Tufted – SvilNeuron olfactory bulbTbx2189
4 Medium Spiny NeuronsStriatal Medium Spiny NeuronsNeuron striatumDrd2, Ppp1r1b6106
5 CTX PyrL2/L3 Pappa2Cortex Layer2/Layer 3 Pyramidal – Satb1Neuron cortexNtf369
6 CTX PyrL2/L3/L4 Ntf3Cortex Layer 2/Layer3/Layer 4 Pyramidal – Ntf3Neuron cortexRasgrf21446
7 CTX PyrL2/L3 MetCortex Layer 2/Layer 3 Pyramidal MetNeuron cortexRasgrf2, Pvrl3, Cux21880
8 CTX PyrL4 Wnt5bCortex Layer 4 Pyramidal – Wnt5bNeuron cortexSlc17a6, Satb2, Sema3c255
9 CTX PyrL2/L3/L4 Mef2cCortex Layer 2/Layer3/Layer 4 Pyramidal – Mef2cNeuron cortexRasgrf2, Pvrl3, Cux2, Rorb8332
10 CTX PyrL4 RorbCortex Layer 4 Pyramidal – RorbNeuron cortexThsd7a, Rorb, Cux2, Pvrl3, Rasgrf2779
11 CTX PyrL4/L5Cortex Layer 4/Layer 5 PyramidalNeuron cortexThsd7a2831
12 CTX PyrL5 Itgb3Cortex Layer 5 Pyramidal – Itbg3Neuron cortexRorb, Thsd7a, Sulf2, Kcnk2,Grik3, Etv1198
13 CTX PyrL5 Fezf2Cortex Layer 5 Pyramidal – Fezf2 Neuron cortexKcnk2, Grik3, Foxp2, Tle4, Tmem200a, Glra2, Etv1352
14 CTX PyrL6aCortex Layer 6a PyramidalNeuron cortexGrik31498
15 CTX PyrL5/L6 Sulf1Cortex Layer 5/Layer 6 Pyramidal – Sulf1Neuron cortexSulf2,Grik3, Tle4, Htr1f, Sulf1493
16 CTX PyrL5/L6 Npr3Cortex Layer 5/Layer 6 Pyramidal – Npr3Neuron cortexGrik3, Tle4, Rxfp1550
17 CTX PyrL6Cortext Layer 6 Pyramidal – Htr1fNeuron cortexSyt6, Grik3, Foxp2, Tle4, Htr1f3479
18 CLAU PyrClaustrum PyramidalNeuron cortexNr4a2140
19 MTt GlutMesencephalic Tectum GlutamatergicNeuron rostral midbrainTfap2d, Slc17a6736
20 THAL GlutThalamic GluatamatergicNeuron thalamusLef1, Tcf7l2, Cacna1g,S lc17a6, Wnt32627
21 THAL Int Six3Thalamic InterneuronNeuron thalamusSix3, Gad1, Gad2202
22 Purkinje EarlyPurkinje EarlyNeuron cerebellumPcp2, Pde1c208
23 Purkinje LatePurkinje LateNeuron cerebellumPcp2, Slc9a3171
24 CB Int ProgenitorCerebellar Interneuron ProgenitorNeuron cerebellumPax3, Mki67160
25 CB Granule PrecursorCerebellar Granule PrecursorNeuron cerebellumGli24364
26 CB Int Stellate/BasketCerebellar Interneuron – Stellate and BasketNeuron cerebellumRora459
27 CB Int Golgi/Stellate/BasketCerebellar Interneuron – Golgi, Stellate and BasketNeuron cerebellumTfap2b420
28 CB GranuleCerebellar GranuleNeuron cerebellumGabra610996
29 CB Int PrecursorCerebellar Interneuron PrecursorNeuron cerebellumPax2851
30 MD Glyc IntMedulla Glycinergic Interneuron – Rxfp2Neuron medullaStac, Slc6a5, Glra1329
31 MD Int Rxfp2Medulla Interneuron – Rxfp2Neuron medullaStac282
32 Nigral DopaminergicNigral DopaminergicNeuron basal gangliaSlc6a347
33 HIPP Pyr Cr2Hippocampal Pyramidal – Cr2Neuron hippocampusCr2232
34 SUB PyrSubiculum PyramidalNeuron hippocampusNtm, Rxfp1, Nr4a278
35 HIPP Pyr CrymHippocampal Pyramidal – CrymNeuron hippocampusCrym1260
36 HIPP Granule Mki67Hippocampus Granule Progenitor Mki67Neuron hippocampusProx1, Mki67657
37 HIPP Pyr PrecursorHippocampal Pyramidal PrecursorNeuron hippocampusNrp1, Zbtb20315
38 HIPP Pyr Grik4Hippocampal Pyramidal – Grik4Neuron hippocampusGrik4, Slc17a7625
39 HIPP Granule Nrp2Hippocampal Granule Precursor – Nrp2Neuron hippocampusProx1, Nrp2515
40 HIPP Granule/PyrCA3Hippocampal Granule/Pyramidal CA3Neuron hippocampusProx1, Slc17a7772
41 HIPP Pyr Npy2rHippocampal Pyramidal – Npy2rNeuron hippocampusNpy2r, Slc17a7117
42 SC Glut Hmga2Spinal Cord Glutamatergic – Hmga2Neuron spinal cordSlc17a6, Slc17a8231
43 SC Glut Gna14Spinal Cord Glutamatergic Gna14Neuron spinal cordSlc17a8, Gna1495
44 Migrating Int Lhx6Migrating Interneuron – Lhx6Neuron migrating interneuronDlx family, Lhx63907
45 Migrating Int TrdnMigrating Interneuron – TrdnNeuron migrating interneuronDlx family, Trdn246
46 Migrating Int Cpa6Migrating Interneuron – Cpa6Neuron migrating interneuronDlx family, Cpa62166
47 Migrating Int Foxp2Migrating Interneuron – Foxp2Neuron migrating interneuronDlx family, Foxp2701
48 Migrating Int Pbx3Migrating Interneuron – Pbx3Neuron migrating interneuronDlx family, Pbx31835
49 Migrating Int Lgr6Migrating Interneuron – Lgr6Neuron migrating interneuronDlx family, Lgr6484
50 Migrating Int Adarb2Migrating Interneuron – Adarb2Neuron migrating interneuronDlx family, Adarb47
51 SVZ StemSubventricular Zone Stem CellNeuron otherGfap, Vim, Nes, Dlx family182
52 Cajal-RetziusCajal-RetziusNeuron otherTrp73, Reln133
53 UnresolvedUnresolvedNeuron other 36469
54 Unresolved Kcng1UnresolvedNeuron other 90
59 Oligo COP1Oligodendroctye Myelinating 2OligodendrocyteOpalin721
60 Oligo COP2Oligodendroctye Myelinating 1OligodendrocyteOpalin1781
58 Oligo NFOL1Oligodendrocyte MatureOligodendrocyteHapln2191
56 Oligo MFOL1Oligodendroctye Newly Formed 1OligodendrocyteTmem2467
55 Oligo MFOL2Committed Oligodendroctye Precursor Cells 1OligodendrocyteGpr17811
57 Oligo MOLCommitted Oligodendroctye Precursor Cells 2OligodendrocyteBcas1323
61 OPCOligodendroctye Precursor CellsOPCPdgfra5793
62 MacrophagePerivivascular MacrophageImmuneDab263
63 MicrogliaMicrogliaImmuneTgfbr1558
64 EndotheliaEndotheliaVasculatureFlt1, Kdr561
65 SMCSmooth Muscle CellsVasculatureAbcc9, Pdgfrb98
66 VLMC Slc6a13Vascular and Leptomeningeal Cells 2VLMCSlc6a131223
67 VLMC Slc47a1Vascular and Leptomeningeal Cells 1VLMCSlc47a1, Slc47a2251
68 Astro Slc7a10Astrocyte – Slc7a10AstrocyteSlc7a103569
69 Astro Prdm16Astrocyte – Prdm16AstrocytePrdm168103
70 Astro GfapAstrocyte – GfapAstrocyteGfap282
71 Bergmann GliaBergman GliaAstrocyteGria11527
72 EpendymaEpendymaEpendymaDnah1/2/5/9/10/11518
73 OECOlfactory Ensheathing Cells (OEC)Schwann CellsLama4, Col5a2, Runx1256
Adapted from Rosenberg et al., 2018 Table S3