Neonatal whole brain | BrainPalmSeq

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 ID	Cluster Name	Class	Marker Genes from Literature	Number Cells
1 OB Mitral/Tufted Eomes	Olfactory Bulb Mitral and Tufted – Eomes	Neuron olfactory bulb	Tbx21	117
2 OB Mitral/Tufted Ms4a15	Olfactory Bulb Mitral and Tufted – Ms4a15	Neuron olfactory bulb	Tbx21	271
3 OB Mitral/Tufted Svil	Olfactory Bulb Mitral and Tufted – Svil	Neuron olfactory bulb	Tbx21	89
4 Medium Spiny Neurons	Striatal Medium Spiny Neurons	Neuron striatum	Drd2, Ppp1r1b	6106
5 CTX PyrL2/L3 Pappa2	Cortex Layer2/Layer 3 Pyramidal – Satb1	Neuron cortex	Ntf3	69
6 CTX PyrL2/L3/L4 Ntf3	Cortex Layer 2/Layer3/Layer 4 Pyramidal – Ntf3	Neuron cortex	Rasgrf2	1446
7 CTX PyrL2/L3 Met	Cortex Layer 2/Layer 3 Pyramidal Met	Neuron cortex	Rasgrf2, Pvrl3, Cux2	1880
8 CTX PyrL4 Wnt5b	Cortex Layer 4 Pyramidal – Wnt5b	Neuron cortex	Slc17a6, Satb2, Sema3c	255
9 CTX PyrL2/L3/L4 Mef2c	Cortex Layer 2/Layer3/Layer 4 Pyramidal – Mef2c	Neuron cortex	Rasgrf2, Pvrl3, Cux2, Rorb	8332
10 CTX PyrL4 Rorb	Cortex Layer 4 Pyramidal – Rorb	Neuron cortex	Thsd7a, Rorb, Cux2, Pvrl3, Rasgrf2	779
11 CTX PyrL4/L5	Cortex Layer 4/Layer 5 Pyramidal	Neuron cortex	Thsd7a	2831
12 CTX PyrL5 Itgb3	Cortex Layer 5 Pyramidal – Itbg3	Neuron cortex	Rorb, Thsd7a, Sulf2, Kcnk2,Grik3, Etv1	198
13 CTX PyrL5 Fezf2	Cortex Layer 5 Pyramidal – Fezf2	Neuron cortex	Kcnk2, Grik3, Foxp2, Tle4, Tmem200a, Glra2, Etv1	352
14 CTX PyrL6a	Cortex Layer 6a Pyramidal	Neuron cortex	Grik3	1498
15 CTX PyrL5/L6 Sulf1	Cortex Layer 5/Layer 6 Pyramidal – Sulf1	Neuron cortex	Sulf2,Grik3, Tle4, Htr1f, Sulf1	493
16 CTX PyrL5/L6 Npr3	Cortex Layer 5/Layer 6 Pyramidal – Npr3	Neuron cortex	Grik3, Tle4, Rxfp1	550
17 CTX PyrL6	Cortext Layer 6 Pyramidal – Htr1f	Neuron cortex	Syt6, Grik3, Foxp2, Tle4, Htr1f	3479
18 CLAU Pyr	Claustrum Pyramidal	Neuron cortex	Nr4a2	140
19 MTt Glut	Mesencephalic Tectum Glutamatergic	Neuron rostral midbrain	Tfap2d, Slc17a6	736
20 THAL Glut	Thalamic Gluatamatergic	Neuron thalamus	Lef1, Tcf7l2, Cacna1g,S lc17a6, Wnt3	2627
21 THAL Int Six3	Thalamic Interneuron	Neuron thalamus	Six3, Gad1, Gad2	202
22 Purkinje Early	Purkinje Early	Neuron cerebellum	Pcp2, Pde1c	208
23 Purkinje Late	Purkinje Late	Neuron cerebellum	Pcp2, Slc9a3	171
24 CB Int Progenitor	Cerebellar Interneuron Progenitor	Neuron cerebellum	Pax3, Mki67	160
25 CB Granule Precursor	Cerebellar Granule Precursor	Neuron cerebellum	Gli2	4364
26 CB Int Stellate/Basket	Cerebellar Interneuron – Stellate and Basket	Neuron cerebellum	Rora	459
27 CB Int Golgi/Stellate/Basket	Cerebellar Interneuron – Golgi, Stellate and Basket	Neuron cerebellum	Tfap2b	420
28 CB Granule	Cerebellar Granule	Neuron cerebellum	Gabra6	10996
29 CB Int Precursor	Cerebellar Interneuron Precursor	Neuron cerebellum	Pax2	851
30 MD Glyc Int	Medulla Glycinergic Interneuron – Rxfp2	Neuron medulla	Stac, Slc6a5, Glra1	329
31 MD Int Rxfp2	Medulla Interneuron – Rxfp2	Neuron medulla	Stac	282
32 Nigral Dopaminergic	Nigral Dopaminergic	Neuron basal ganglia	Slc6a3	47
33 HIPP Pyr Cr2	Hippocampal Pyramidal – Cr2	Neuron hippocampus	Cr2	232
34 SUB Pyr	Subiculum Pyramidal	Neuron hippocampus	Ntm, Rxfp1, Nr4a2	78
35 HIPP Pyr Crym	Hippocampal Pyramidal – Crym	Neuron hippocampus	Crym	1260
36 HIPP Granule Mki67	Hippocampus Granule Progenitor Mki67	Neuron hippocampus	Prox1, Mki67	657
37 HIPP Pyr Precursor	Hippocampal Pyramidal Precursor	Neuron hippocampus	Nrp1, Zbtb20	315
38 HIPP Pyr Grik4	Hippocampal Pyramidal – Grik4	Neuron hippocampus	Grik4, Slc17a7	625
39 HIPP Granule Nrp2	Hippocampal Granule Precursor – Nrp2	Neuron hippocampus	Prox1, Nrp2	515
40 HIPP Granule/PyrCA3	Hippocampal Granule/Pyramidal CA3	Neuron hippocampus	Prox1, Slc17a7	772
41 HIPP Pyr Npy2r	Hippocampal Pyramidal – Npy2r	Neuron hippocampus	Npy2r, Slc17a7	117
42 SC Glut Hmga2	Spinal Cord Glutamatergic – Hmga2	Neuron spinal cord	Slc17a6, Slc17a8	231
43 SC Glut Gna14	Spinal Cord Glutamatergic Gna14	Neuron spinal cord	Slc17a8, Gna14	95
44 Migrating Int Lhx6	Migrating Interneuron – Lhx6	Neuron migrating interneuron	Dlx family, Lhx6	3907
45 Migrating Int Trdn	Migrating Interneuron – Trdn	Neuron migrating interneuron	Dlx family, Trdn	246
46 Migrating Int Cpa6	Migrating Interneuron – Cpa6	Neuron migrating interneuron	Dlx family, Cpa6	2166
47 Migrating Int Foxp2	Migrating Interneuron – Foxp2	Neuron migrating interneuron	Dlx family, Foxp2	701
48 Migrating Int Pbx3	Migrating Interneuron – Pbx3	Neuron migrating interneuron	Dlx family, Pbx3	1835
49 Migrating Int Lgr6	Migrating Interneuron – Lgr6	Neuron migrating interneuron	Dlx family, Lgr6	484
50 Migrating Int Adarb2	Migrating Interneuron – Adarb2	Neuron migrating interneuron	Dlx family, Adarb	47
51 SVZ Stem	Subventricular Zone Stem Cell	Neuron other	Gfap, Vim, Nes, Dlx family	182
52 Cajal-Retzius	Cajal-Retzius	Neuron other	Trp73, Reln	133
53 Unresolved	Unresolved	Neuron other		36469
54 Unresolved Kcng1	Unresolved	Neuron other		90
59 Oligo COP1	Oligodendroctye Myelinating 2	Oligodendrocyte	Opalin	721
60 Oligo COP2	Oligodendroctye Myelinating 1	Oligodendrocyte	Opalin	1781
58 Oligo NFOL1	Oligodendrocyte Mature	Oligodendrocyte	Hapln2	191
56 Oligo MFOL1	Oligodendroctye Newly Formed 1	Oligodendrocyte	Tmem2	467
55 Oligo MFOL2	Committed Oligodendroctye Precursor Cells 1	Oligodendrocyte	Gpr17	811
57 Oligo MOL	Committed Oligodendroctye Precursor Cells 2	Oligodendrocyte	Bcas1	323
61 OPC	Oligodendroctye Precursor Cells	OPC	Pdgfra	5793
62 Macrophage	Perivivascular Macrophage	Immune	Dab2	63
63 Microglia	Microglia	Immune	Tgfbr1	558
64 Endothelia	Endothelia	Vasculature	Flt1, Kdr	561
65 SMC	Smooth Muscle Cells	Vasculature	Abcc9, Pdgfrb	98
66 VLMC Slc6a13	Vascular and Leptomeningeal Cells 2	VLMC	Slc6a13	1223
67 VLMC Slc47a1	Vascular and Leptomeningeal Cells 1	VLMC	Slc47a1, Slc47a2	251
68 Astro Slc7a10	Astrocyte – Slc7a10	Astrocyte	Slc7a10	3569
69 Astro Prdm16	Astrocyte – Prdm16	Astrocyte	Prdm16	8103
70 Astro Gfap	Astrocyte – Gfap	Astrocyte	Gfap	282
71 Bergmann Glia	Bergman Glia	Astrocyte	Gria1	1527
72 Ependyma	Ependyma	Ependyma	Dnah1/2/5/9/10/11	518
73 OEC	Olfactory Ensheathing Cells (OEC)	Schwann Cells	Lama4, Col5a2, Runx1	256

Adapted from Rosenberg et al., 2018 Table S3