RNA was extracted from iPSCs, HLCs, and primary human hepatocytes using the miRNeasy Mini Kit (QIAGEN), and RNA integrity was assayed using the RNA 6000 Nano Kit (Agilent) on the Agilent Bioanalyzer system. All samples had an RNA integrity number (RIN) greater than 7.5. Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed at the Next Generation Sequencing Center of the University of Pennsylvania on Illumina HiSeq 2000/2500 systems with paired-end, 100-bp/125-bp read lengths with a target read depth of 50 million reads per sample. We generated and used whole transcriptome data (RNA-seq) for a total of 89 iPSC samples and 86 HLC samples. All individuals included had both iPSCs and HLCs generated for the study except for five individuals (one iPSC-only and four HLC-only).
