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

From: Single-cell RNA-sequencing of the brain

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]
  1. 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