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. 2022 Dec 2;3(2):100232. doi: 10.1016/j.xgen.2022.100232
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Human peripheral blood mononuclear cell N/A N/A
Chemicals, peptides, and recombinant proteins
RPMI 1640 Medium SIGMA MDL# R0883-500ML
Fetal Bovine Serum PAN BIOTECH Cat# P30-5500
Dulbecco’S Phosphate Buffered Saline PAN BIOTECH Cat# P04-36500
Buffer EB QIAGEN Cat# 19086
SPRIselect Beckmann Coulter Cat# B23318
Critical commercial assays
Chromium Next GEM Single Cell 3′Regent Kits v3.1 10X CG000315 Rev A
Chromium Next GEM Single Cell ATAC Regent Kits v1.1 10X CG000209 Rev D
High sensitivity DNA kit Agilent Cat# 5067-4626
Deposited data
Human reference genome NCBI build 38, GRCh38 Genome Reference Consortium48 http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/
Human reference epigenomic annotations Roadmap Epigenomics Consortium31 https://egg2.wustl.edu/roadmap/web_portal/index.html
Bulk RNA-seq eQTL summary statistics (release 2019-12-11) eQTL-Gen Consortium33 https://www.eqtlgen.org
GTEx eQTL summary statistics (v8) GTEx v828 https://www.gtexportal.org/home/datasets
Promoter capture HiC results Javierre et al.32 https://osf.io/u8tzp/
COVID-19 GWAS summary statistics (release round 6) The COVID-19 Host Genetics initiative12 https://www.covid19hg.org/results/r6
snRNA-seq data Wendisch et al.25 EGAS00001004928; EGAS00001005634; https://nubes.helmholtz-berlin.de/s/XrM8igTzFTFSoio
snRNA-seq data This paper EGAS00001006559
snATAC-seq data This paper EGAS00001006560
Genotypes This paper EGAZ00001823187
Software and algorithms
Plink v1.90b6.21 64-bit (19 Oct 2020) Chang et al.49 https://www.cog-genomics.org/plink/
R 4.1 R Core Team https://www.r-project.org/
R package Seurat version 3.2.2 Stuart et al.50 https://cran.r-project.org/web/packages/Seurat/index.html
R package ArchR version 1.0.1 Granja et al.51 https://www.archrproject.com/
R package ggplot2 version 3.3.2 Wickham et al.52 https://cran.r-project.org/web/packages/ggplot2/index.html
R package Bioconductor version 3.12 Gentleman et al.53 https://bioconductor.org
R package clusterProfiler version 4.0.5 Yu et al.54 https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
R package ggpubr version 0.4.0 Kassambara, The Comprehensive R Archive Network (CRAN) https://cran.r-project.org/web/packages/ggpubr/index.html
R package pheatmap version 1.0.12 Raivo, The Comprehensive R Archive Network (CRAN) https://cran.r-project.org/web/packages/pheatmap/index.html
R package tidyverse version 1.3.0 Wickham et al.52 https://CRAN.R-project.org/package=tidyverse
R package org.Hs.eg.db version 3.12.0 Carlson55 https://bioconductor.org/packages/3.12/data/annotation/html/org.Hs.eg.db.html
R package ggrepel version 0.9.0 Slowikowski56 https://cran.r-project.org/web/packages/ggrepel/index.html
R package data.table version 1.14.0 Dowle57 https://cran.r-project.org/web/packages/data.table/index.html
R package GenomicInteractions version 1.30.0 Harmston et al.58 https://bioconductor.org/packages/release/bioc/html/GenomicInteractions.html
R package GViz version 1.20.1 Hahne and Ivanek59 https://bioconductor.org/packages/3.15/bioc/html/Gviz.html
R package motifbreakR version 2.10.0 Coetzee, Coetzee, and Hazelett30 https://bioconductor.org/packages/release/bioc/html/motifbreakR.html
Python version 3.9.6 Van Rossum60 https://www.python.org
Python package MACS2 version 2.2.7 Gaspar61 https://pypi.org/project/MACS2/
Bowtie2 version 2.4.4 Langmead and Salzberg62 N/A
Python package matplotlib version 3.4 Hunter63 https://matplotlib.org
Python package pysam version 0.17.0 Github pysam-developers https://github.com/pysam-developers/pysam
BCFtools version 1.12 Danecek et al.64 http://www.htslib.org
SAMtools version 1.12 Danecek et al.64 http://www.htslib.org
Htslib version 1.12 Danecek et al.64 http://www.htslib.org
WASP pipeline version 0.3.4 van de Geijn et al.65 https://github.com/bmvdgeijn/WASP
GATK/ASEReadCounter version 4.2.0.0 Castel et al.66 https://gatk.broadinstitute.org
VEP (online) McLaren et al.67 https://www.ensembl.org/Tools/VEP
TOPMed and Michigan Imputation server Fuchsberger, Abecasis, and Hinds; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium et al.; Das et al.68,69,70 https://imputation.biodatacatalyst.nhlbi.nih.gov;
https://imputationserver.sph.umich.edu
Original codes and scripts This paper https://doi.org/10.5281/zenodo.7270242