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Table 1 Overview of recent brain scRNA-seq studies

From: Single-cell RNA-sequencing of the brain

Brain region Isolation method RT and cDNA amplification # of cells sequenced Major populations identified # of cells in population Subpopulations identified Refs.
Primary visual cortex FACS SMARTer 1600 GABAergic neurons 761 23 [21]
Glutamatergic neurons 764 19
Non-neuronal 103 7
Somatosensory cortex, hippocampal CA1 Fluidigm, FACS STRT/C1 3005 S1 pyramidal neurons 390 8 [8]
CA1 pyramidal neurons 961 4
Interneurons 300 16
Oligodendrocytes 811 6
Astrocytes 210 2
Microglia 90 5
Vascular endothelial cells 180 2
Mural cells 60 2
Ependymal cells 30 2
Hippocampal dentate gyrus Pippeting SMART-seq 168 CFPnunc qNSC or NPCs 132 6 [73]
CFPnuc− non-NPCs 26 5
Striatum Fluidigm, FACS SMART-seq2, SMARTer 1208 Neurons (D1-MSN, D2-MSN, interneurons) 368 3 [74]
Astrocytes 107 1
Oligodendrocytes: newly formed (NFO), mature (MO) 43 2
Stem cells (NSC, OPC) 20 2
Vascular cells (VSMCs, Endothelial) 43 2
Immune cells (microglia, macrophage) 119 2
Ependymal (ciliated, secretory) 39 2
Somatosensory cortex, dentate gyrus, hippocampus CA1, corpus callosum, amygdala, hypothalamus, zona incerta, SN-VTA, dorsal horn Fluidigm, FACS STRT/C1 5072 Oligodendrocyte precursor cells (OPC) 310 1 [75]
Committed oligodendrocyte precursors (COP) 140 1
Newly formed oligodendrocytes (NFOL1, NFOL2) 219, 293 2
Myelin-forming oligodendrocytes (MFOL1, MFOL2) 353, 933 2
Mature oligodendrocytes (MOL1, …, MOL6) 126, …, 835 6
Vascular and leptomeningeal cells (VLMC) 76 1
  1. qNSC quiescent neural stem cells, NPC neural precursor cells, MSN medium spiny neurons, NSC neural stem cell