Chunk #60 — STAR*METHODS — METHOD DETAILS — Differential gene expression among iPSCs, HLCs, and GTEx livers

Source

Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci.

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Text

For differential gene expression analyses, gene expression estimates (TPM) were log-transformed after the addition of a constant (1) to each expression estimate. The top 58% (27,446 genes) most highly expressed genes across cell types (mean expression in iPSCs, HLCs, primary hepatocytes, and whole livers) were used for genome-wide PCA using the pcaMethods R package (Stacklies et al., 2007).