PRMT-APA README
This repository contains the scripts and data files necessary to generate the figures from "PRMT activity promotes global 3' UTR shortening in proliferating cells" (Griffith et al., 2025, doi: https://doi.org/10.1101/2025.03.06.641848)
RAW DATA
The data generated in this study has been deposited at EBI ArrayExpress under the following accession numbers:
- “E-MTAB-14928” (96hrs ADMAi vs SDMAi vs SDMAi+ADMAi)
- “E-MTAB-14927” (DMAi timecourse)
- “E-MTAB-14932” (DMAi across panel of 10 cancer lines)
- “E-MTAB-14990” (murine T cells)
- “E-MTAB-14992” (patient-derived organoids)
- “E-MTAB-14930” (siCFIm25 +/- DMAi)
The fastq files present in each of these datasets were processed using the nf-quantseq pipeline (v.0.1.0; DOI: 10.5281/zenodo.14417140), which generates Count bed files and a poly(A) site atlas - all of which are located in the Data/ directories in this repository, organised by Figure. These files were used as input for the DRIMseq.R scripts which were the starting point for all APA analyses performed in the manuscript.
REPRODUCING ANALYSES FROM MANUSCRIPT
Scripts used to produce the figures from the manuscript are located in the Scripts/ directory within this repository, organised by Figure number. Files required for each script are located in the Data/ directory also found in this repository, organised by figure. Following each initial DRIMSeq analysis, APA events were next classified using the classification_of_APA_events.R script, before all other dataset-specific secondary analyses were peformed. For the more complex scripts located in this repository, script-specific READMEs can be found in the same directories as those scripts.
CONTACT
Contact llywelyn.griffith@kcl.ac.uk if you have any questions.