Snakemake/R/Pyhton code used for total RNA-Seq analysis of Jaeger et al. "Chemically-induced protein degradation reveals 1 inflammation-dependent requirement for TREG lineage-defining transcription factor FOXP3". Submitted, 2025. Christina Jäger, Polina Dimitrova1, Qiong Sun, Jesse Tennebroek, Elisa Marchiori, Markus Jaritz, Rene Rauschmeier, Guillem Estivill, Anna Obenauf, Meinrad Busslinger, Joris van der Veeken, van der Veeken lab
- Snakefile contains the Snakemake file to run the individual analyses.
- rTregaTreg contains snakemake config file and sample tables for analysing differential gene expression in steady-state or activated GFP+ CD4 T cells isolated from pooled secondary lymphoid tissues of animals treated with 5-Ph-IAA or PBS, all normalized together.
- rTregaTreg_byCellType contains snakemake config file and sample tables for analysing differential gene expression in steady-state or activated GFP+ CD4 T cells isolated from pooled secondary lymphoid tissues of animals treated with 5-Ph-IAA or PBS, with celltypes normalized individually.
- Treg_Il2aIl2 contains snakemake config file and sample tables for analysing differential gene expression for differentially expressed genes in GFP+ TREG cells isolated from mice injected with IL-2/anti-IL2 complexes with or without 5-Ph-IAA.
- code contains additinonal R and python code for the individual processing steps.
Note: these scripts are optimized for runnig on the Vienna Biocenter Computing cluster (CBE) using SLURM.
Original implementation: Kimon Froussios
Updates/changes (adding all-noexon and UMI handling): Markus Jaritz, van der Veeken lab