🧬 Project Overview

Welcome to the code repository for the alternative splicing analysis of the paper:

📄 TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors

This repository houses the code used to generate the plots in Figure 6 presented in the paper. The code is organised into R quarto notebooks. Two notebooks perform the alternative splicing analysis in the TAF2 and SRRM2 Knockdown datasets, respectively, and one main notebook integrates the data and generates the panels for the publication.

Tip

For easy access to each analysis report, visit our main homepage with direct links to the analysis reports: 🔗 Main Homepage

Feel free to explore the code and reproduce our findings! 🌟

If you use our work, please cite us appropriately.

📖 Citations

Cell Report

Bhuiyan T.^†, Arecco N.², Mendoza Sanchez P.K.², Kim J., Schwan C., Weyrauch S., Nizamuddin S., Prunotto A., Tekman M., Biniossek M.L., Koidl S., Drepper F., Huesgen P.F., Grosse R., Hugel T., Arnold S.J.^† (2024). TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing factors Cell Report. DOI: 10.1016/j.celrep.2025.115616 ^† Co-correspondence ² Co-second

BioRχiv

Bhuiyan T.^†, Mendoza Sanchez P.K., Arecco N., Kim J., Nizamuddin S., Prunotto A., Tekman M., Biniossek M.L., Koidl S., Hugel T., Arnold S.J.^† (2024). TAF2 condensation in nuclear speckles links basal transcription factor TFIID to RNA splicing BioRχiv. DOI: 10.1101/2024.02.05.578926 ^† Co-correspondence

Related links

• 💡CUT&RUN and RNA-seq fastq files (NCBI GEO, SRA Run Selector).