The University of Sheffield
108 files

Widespread 3’ UTR splicing regulates expression of oncogene transcripts in sequence-dependent and independent manners

RNA-seq data from 7897 TCGA cancer and normal tissue samples were used to generate a cancer specfic transcript assembly using stringtie.

We used a custom algorithm based on comparison the a filtered reference transcriptome to annotate transcripts that contained introns in the 3' UTR. This assembly was then used to quantitate the same samples using Salmon to produce per transcript, per patient expression levels. The fractional expression of each transcript was calculated as transcript expression divided by gene expression. rMATs was used to calculate the change in retained intron usage between normal and cancer samples on a custom event set based on the previously identified 3' UTR introns. The counts of reads compatible and incompatible with splicing for these introns from each sample was also recorded. Finally feature counts was used to count reads mapping to each exon on junction counts of each intron.


Regulation of transcript stability by splicing in non-coding gene regions

Biotechnology and Biological Sciences Research Council

Find out more...

Mechanistic Biology and its strategic application

Biotechnology and Biological Sciences Research Council

Find out more...



  • There is no personal data or any that requires ethical approval


  • The data complies with the institution and funders' policies on access and sharing

Sharing and access restrictions

  • The uploaded data can be shared openly

Data description

  • The file formats are open or commonly used

Methodology, headings and units

  • There is a file including methodology, headings and units, such as a readme.txt

Usage metrics

    School of Biosciences



    Ref. manager