Transcriptome analysis of human and chimpanzee iPS cells

mRNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). To compare gene expression levels, the reads were first mapped to the chimpanzee genome (panTro5), and mapped reads were then mapped to the human genome (hg38). Gene expression was anlyzed based on the hg38 annotation. Overall design: Two human and two chimpanzee iPS cell lines (all are females and 36 to 43 years old) were cultured in the same condition. RNAs were then extracted, and strand-specific poly(+) RNA sequencing libraies were made for HiSeq sequencing in the 150-bp paired-end mode.