Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation
This is the github repository of our paper Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation.
High throughput sequencing data have been deposited to Array Express under accession number E-MTAB-8851. ChIP-chip data have been deposited to Array Express under accession number E-MTAB-8793. Other data and source codes are available upon request.
The workflow was written with snakemake (python), and need some genomic tools :
bwa 0.7.12-r1039.samtools 1.9.FastQC v0.11.5.macs2 2.1.2.bedtools v2.26.0.deeptools 3.4.3.R version 3.6.3.
the scripts were written with R, and need some packages
:
library(rtracklayer).library(BSgenome.Hsapiens.UCSC.hg19).library(ggplot2).library(reshape2).library(dplyr).library(Homo.sapiens).
| Scripts | Description | Figures |
|---|---|---|
| plot_4C_withotherdata.R | Compute the HiC matrix / ChIP-seq gammaH2AX / 4C-seq / insulation score / TAD border / CTCF peaks for given regions | Figs 1d; ext1e |
| make_APA_heatmap.R | Get the APA from juicer tools and produce graphics with ggplot2. | Figs 2c; ext2f; ext2g; ext6f |
| make_gamma_boxplot_cinetique.R | Compute the speed for gammaH2AX progression over TAds and show distance distribution over time. | Figs ext5b |
| make_4Cseq_barplot.R | Compute differential 4C-seq signal (log2 +DSB/-DSB) on 1mb around DSBs viewpoints. | Figs ext4c; ext3d; ext3h |
| make_chipseq_barplot_TADs.R | Compute ChIP-seq quantification within the damaged TAD and neighboring TADs. | Figs ext1f |
| make_chipseq_boxplot_cohesine.R | Compute signal over cohesine peaks. | Figs ext6b |
| make_chipseq_boxplot_profile.R | Compute signal over DSBs and produce some profiles/boxplots. | Figs ext1d; ext1k; 2e; ext2b; ext7b |
| make_HiC_heatmap.R | Compute average heatmaps from HiC dumped matrixes (juicer) and HiTC. | Figs 2b; 2d; 2g; ext2d; ext2e |
| make_HiTC.R | Produce HiTC format from dumped matrix to be loaded in R. | |
| make_loopanchor_chipseq_boxplot_over_distance.R | Compute the quantification of SCC1 recruitment on loop anchors at different distances from DSBs. | Figs ext6d |
| make_loopanchor_chipseq_boxplot.R | Compute the ChIP-seq signal on loop anchors. | Figs ext7c |
| make_loopanchor_HiC_boxplot.R | Compute the differential loop strength in undamaged or damaged TADs | Figs ext6g |
| plot_gH2AX_TADborder.R | Compute average gammaH2AX profile centered to the closest TAD border to the DSBs. | Figs 1e |