Genome-wide analysis of cell cycle-specific SF3B1-chromatin interactions and its effect on RNA splicing

We report genome-wide analysis of SF3B1-chromatin interactions in cell cycle synchronized HeLa cells. ChIP-Seq was performed on cell-cycle synchronized HeLa Cell for SF3B1 (G1S and G2M) in duplicates. RNA-Seq was performed on same cells, also in duplicates to determine changes in gene expression and RNA splicing. ChIP-Seq files were aligned to hg19 and peaks calls and comparisons performed by HOMER. RNA-Seq datasets were aligned using STAR aligner and differential expression determined by Cufflinks package. Alternative splicing was determined by rMATS algorithm Overall design: Determination of cell cycle specific changes in chromatin interaction of SF3B1 through SF3B1 ChIP-Seq and correlate results with changes in RNA expression and splicing with RNA-Seq from same samples