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

We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. 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). RNA-seq gene expression analyses in diverse mouse and human samples.