Chunk #59 — STAR Methods — Quantification and Statistical Analysis — Defining pseudotime and differentiation stage in single cells

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Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

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Data from each cell was log transformed by taking Log2(FPKM+1), and absent genes (FPKM>1 in >5% of in vitro cells) were excluded from the analysis. Next, standard principal component analysis (PCA) was performed (using the prcomp R function) on the top 1% most differential genes based on maximum pairwise fold change across eight groups (DCX+ D24, DCX− D24, DCX+ D54, DCX− D54, DCX+ D100, DCX− D100, DCX+ D125, DCX− D125). Differentiation stage and pseudotime were defined as the first two principal coordinates, respectively.