Single-cell RNA-sequencing of the brain

Clinical and Translational Medicine

Table 2 Data analysis methods used in recent brain scRNA-seq studies

Brain region	Expression measure	Clustering	Refs.
Primary visual cortex (L1, 2/3, 4, 5, 6)	RPKM and counts	PCA, WGCNA, random forests	[21]
Somatosensory cortex and hippocampal CA1	CPM	BackSPIN	[8]
Hippocampal dentate gyrus	TPM	Hierarchical clustering, PCA, Waterfall	[73]
Striatum	CPM	2D-tSNE, rPCA	[74]
Somatosensory cortex, striatum, dentate gyrus, hippocampus CA1, corpus callosum, amygdala, hypothalamus, zona incerta, SN-VTA, dorsal horn	CPM	BackSPINv2	[75]

RPKM reads per kilobase of million mapped reads, CPM counts per million mapped reads, TPM transcripts per million mapped reads, PCA principal component analysis, WGCNA weighted gene coexpression network analysis, t-SNE t-distributed stochastic neighbor embedding, rPCA robust principal component analysis