rMATS analysis of alternative splicing events in a mouse model of environmental liver disease

rMATS (https://rnaseq-mats.sourceforge.io/) was used to identify differential alternative splicing events (ASEs) corresponding to all five major types of AS patterns, i.e., skipped exon (SE), mutually exclusive exons (MXE), alternative 3’ splice site (A3SS), alternative 5’ splice site (A5SS), and retained intron (RI), in the HFD-fed mouse livers exposed to Ar1260, PCB126, or Ar1260 + PCB126 co-exposure compared to vehicle control This dataset identifies differential ASEs corresponding to all five major types of AS patterns [i.e., skipped exon (SE), mutually exclusive exons (MXE), alternative 3’ splice site (A3’SS), alternative 5’ splice site (A5’SS), and retained intron (RI)], between Ar1260, PCB126, and Ar1260 + PCB126-exposed samples and vehicle control. For each ASE, the estimation of the alternatively spliced region usage is defined as percent-spliced in (ψ or PSI). Each comparison was made to identify differential ASEs with an associated change in exon usage (∆ψ). Differential ASEs were detected with an FDR of <0.05 and |∆ψ| of≥5%. The difference in the proportion of the two isoforms of the transcript was expressed as the change in mean percentage spliced-inform included (mean ∆ψ).