See the methods file (Rmd or PDF) for a verbose summary of the steps we took to process and analyze the bulk RNA-seq data supporting the manuscript by Regnier-Golanov et al. (2021) including motif analysis and exploration of putative regulators.
The makefile in the folder preprocessing contains all details about the preprocessing, including read alignment and count matrix generation.
For details of the differential gene expression analysis, see the Rmd in deseq2_analysis.
The FASTQ files of the bulk RNA-seq data as well as a spreadsheet with differentially expressed genes can be found on GEO with accession number GSE167110
All scripts were written by Paul Zumbo and Friederike Dündar.
Don't hesitate to get in touch with questions related to the code.
