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 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