README

• This repository contains all source code for analyzing the data and generating the figures in the paper: UTX condensation underlies its tumor suppressive activity
• A README file is attached to each folder/subfolder.

Notes of data analysis

f0_data_process

• QC and process the raw ChIP-seq, RNA-seq and HiChIP datasets, etc.

f2_gene_expression

• identify DEG
• PC analysis

f3_differential_chip_binding

• differential ChIP-seq binding union peaks/islands, gene promoter (TSS+/-2kb, TSS+/-10kb) and gene body
• then check the binding patterns of DEG between Vector and WT

f4_hichip_SICER_looping

• HiChIP data processed using MAPS
• check the length of loops and genomic positions of loop anchors
• check the association between genes and differential loops

f4_hichip_MAPS_new

• HiChIP data processed using MAPS
• using the final selected chip-seq data to call SICER islands
• and use the merged islands as input for MAPS

f5_hichip

• additional hichip analysis
• HiC-Pro + BART3D

f6_proseq

• analysis of proseq data

f7_chipseq

• analysis of final selected QC passed chipseq data
• raw & trimmed data /nv/vol190/zanglab/zw5j/projects_data/UTX_HaoJiang/final_chipseq_merge_trim
• processed data /nv/vol190/zanglab/zw5j/since2019_projects/UTX_HaoJiang/f0_data_process/chip_seq/final_chipseq

f8_integrative_analysis

• integrate expression data, chip-seq binding