Repeat expansions in C9orf72 rewire the 3D chromatin landscape in ALS

This repository contains processed files to understand 3D genomic architecture of C9orf72-mediated ALS.
Files are organized into the following subdirectories:

• Loops_hiPSC_Neuron, Loops_Postmortem_Neuron, and Loops_Postmortem_Glia — Contain 10 kb .cool files for each individual sample (biological replicate) of hiPSC-derived neurons, postmortem neurons, and postmortem glia.
• Loops_count_matrix — Contains count matrices for loops detected in hiPSC-derived neurons, postmortem neurons, and postmortem glia. These matrices serve as input for differential loop analysis.
• RNA-seq — Includes .bigWig files for each sample used in differential gene expression analysis, along with a gene-by-sample count matrix formatted for DESeq2 input.
• CTCF — Contains .bigWig files for differential CTCF peak analysis, as well as a peak-by-sample count matrix formatted for DESeq2 input.
• CHART — Includes .bigWig files for gained CHART peak analysis, a peak-by-sample count matrix used for gained-peak calling, and a .tsv file summarizing total reads per sample.