Genetic variation in correlated regulatory region of Immunity

https://www.biorxiv.org/content/10.1101/2022.07.21.500922v1

code to replicate the analysis performed in this preprint.

Data

Data downloaded from the European Genome-Phenome Archive

website: https://ega-archive.org/datasets

datasets used:

EGAD00001002663 Illumina HiSeq 2000, 193 samples

EGAD00010000850 DNA methylation profiles of monocytes, neutrophils and T cells from 525 healthy donors

EGAD00001002675 RNA-Seq data for 205 mature neutrophil sample(s)

EGAD00001002670 ChIP-Seq data for 182 mature neutrophil sample(s).

EGAD00001002671 RNA-Seq data for 212 CD4-positive, alpha-beta T cell sample(s).

EGAD00001002673 ChIP-Seq data for 154 CD4-positive, alpha-beta T cell sample(s).

EGAD00001002672 ChIP-Seq data for 172 CD14-positive, CD16-negative classical monocyte sample(s).

EGAD00001002674 RNA-Seq data for 197 CD14-positive, CD16-negative classical monocyte sample(s).

and Hi-C data from Javierre et al., Cell 2016

The code and data fir the figures are found in the folder CRD immune cells/A CRDs/R plots

Softwares

Publicly available code used in this study : BCFtools v1.8 (based on HTSlib v1.8) PLINK v1.90b5 R v3.5.1 HOMER v4.9 (webpage: http://homer.ucsd.edu/homer/ngs/peaks.html) Clomics v1.0 (https://github.com/odelaneau/clomics) QTLTools v1.3.1 (https://qtltools.github.io/qtltools) GOrilla for identifying and visualizing enriched GO terms (http://cbl-gorilla.cs.technion.ac.il/)