Ectopic expression of BEX genes in T-cell Acute Lymphoblastic Leukemia : Bioinformatics resources and Docker environments

This repository provides Docker containers designed to reproduce the analyses presented in Quessada, Nozais et al. (2025), along with selected intermediate files. Detailed instructions for reproducing the analysis are available on github (https://github.com/mathisnozais/BEX) and raw data and other intermediate files are available in GEO/SRA (GSE303127 / SRP602355 for the RNAseq and GSE303130 / SRP602362 for the CUT&Tag). This Zenodo hosts the following resources : Docker images used for the analysis (rna431-2.tar and Seurat440paper.tar) Confocal microscopy raw images from PLA experiments (Confocal_images.tar.gz) The thymic single-cell RNA-seq dataset from Park et al. (Science 2019; DOI: 10.1126/science.aay3224), converted from ScanPy to Seurat (Park_dataset.robj) Preprocessed single-cell RNA-seq data (ThymusWT_clean_cc-regressed_noADT.Robj and BC_BEX_mice.Robj) TARGET and TCGA transcriptomic data objects and processed matrices (files named XXX_TARGET_XXX) TO COMPLETE (files named SANDA_GR_X.txt) GSE29180.bed & GSE25000.bed Related to jurkat RNAseq analysis :JKT_CRISPR_featurecounts.txt and dds_CRISPR.rds gencode.v36.annotation.gtf h5ad.tar individual and consensus CUT&Tag peaks for H3K27ac, H3K4me1 and H3K4me3 in Jurkat cell (BEX WT and BEX KO) : CUTandTag_individual_peak_calling.zip & CUTandTag_consensus_peaks.zip i-cisTarget ouputs for differentially modified histones regions (named i-cisTarget_XXXXX.zip) GSEA results for genes associated with differential epigenetic peaks analysed related to the gene expression changes observed in the RNA-seq data for Jurkat cells (BEX KO versus BEX WT) : GSEA_ChIP-histones-gene-sets_VS_RNAseq.txt