TE-derived small RNA analysis of human and chimpanzee iPS cells

Small RNA-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). The human samples were mapped to the human genome (hg38) and the chimpanzee samples were mapped to the chimpanzee genome (panTro5). The mapped reads for individual TE copies (in the repeatmasker tables downloaded from UCSC genome browser) were counted, and those for the same subfamily were summed up. The counts were normalized by RPM (reads per million genome-mapped reads). 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 small RNA sequencing libraies were made for HiSeq sequencing in the 50-bp single-end mode.