CpG island mediated linear and spatial gene partitioning (pA+ RNA-seq profile)

In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009). pA+ RNA-seq gene expression analysis in diverse mouse and human samples.