| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Deposited data | ||
| Genotypes from low-pass whole genome sequencing | This paper | dbGaP: phs002855.v1.p1 |
| Bulk RNA sequencing (raw files and TPMs) | This paper | GEO: GSE225650 |
| eQTL and sQTL summary statistics | This paper | Zenodo: https://doi.org/10.5281/zenodo.7581778 |
| snATAC sequencing (raw and processed data) | This paper | GEO: GSE175621 and GEO: GSE188422 |
| ATAC sequencing and H3K27 Hi-ChIP for human coronary artery smooth muscle cells (HCASMCs) | This paper | GEO: GSE113348 and GEO: GSE101498 |
| GWAS summary statistics for coronary artery disease | Tcheandjieu et al.11 | GWAS catalog: GCST90132305 |
| GWAS summary statistics for myocardial infarction | Hartiala et al.9 | GWAS catalog: GCST011365 |
| GWAS summary statistics for coronary artery disease | Matsunaga et al.10 | GWAS catalog: GCST010480 |
| GWAS summary statistics for coronary artery disease | Koyama et al.8 | Biobank Japan: https://biobankjp.org |
| GWAS summary statistics for coronary artery disease | van der Harst et al.5 | GWAS catalog: GCST005194 |
| GWAS summary statistics for coronary artery calcification | Kavousi et al.105 | GWAS catalog: GCST90278455 and GCST90278456 |
| GWAS summary statistics for lipid traits (HDL, LDL, TC, logTG) | Graham et al.18 | GWAS catalog: GCST90239649, GCST90239655, GCST90239661, and GCST90239673 |
| GWAS summary statistics for blood pressure traits (DBP, SBP, PP) | Evangelou et al.76 | GWAS catalog: GCST006624, GCST006629, and GCST006630 |
| GWAS summary statistics for carotid plaque and IMT | Franceschini et al.106 | GWAS catalog: GCST001231 |
| ENCODE CTCF, H3K27Ac, and H3K4me3 annotations for coronary artery | ENCODE15 | ENCODE Pproject: https://www.encodeproject.org/ |
| GTEx summary statistics for eQTLs in AOR, COR, and TIB tissues | GTEx20 | GTEx Portal: https://www.gtexportal.org/home/ |
| STARNET eQTL summary statistics, gene expression, and clinical trait enrichment for AOR & MAM tissues | Koplev et al.39 | dbGaP: phs001203.v2.p1 http://starnet.mssm.edu/ |
| scRNAseq data for coronary and carotid tissues (integrated single-cell reference) | Verdezoto et al.30; Wirka et al.41; Pan et al.107; Alsaigh et al.108; Hu et al.109 | GEO: GSE131778, GSE155512, and GSE159677. Zenodo: https://doi.org/10.5281/zenodo.6032099 |
| Software and algorithms | ||
| Custom R and shell scripts scripts (data processing; plot generation; coloc, Paintor, SnpEff, SMR, RFMix implementation) | This paper | GitHub: https://github.com/MillerLab-CPHG/CAD_QTL and zenodo: https://doi.org/10.5281/zenodo.10095581 |
| R 4.0.3 | R Core Team | https://www.r-project.org/ |
| R package SNPRelate v1.24.0 | Zheng et al.110 | https://github.com/zhengxwen/SNPRelate |
| Beagle v5.2 | Browning et al.111 | https://bioinformaticshome.com/tools/imputation/descriptions/BEAGLE.html |
| STAR | Dobin et al.112 | https://github.com/alexdobin/STAR/releases |
| samtools v1.10 | Li & Durbin113 | http://samtools.sourceforge.net/ |
| bedtools v2.29.2 | Quinlan et al.114 | https://github.com/arq5x/bedtools2 |
| VCFtools v0.1.16 | Danecek et al.115 | https://vcftools.github.io |
| BCFtools v1.9 | https://doi.org/10.1093/gigascience/giab008 | http://www.htslib.org/ |
| Tabix v0.6 | https://doi.org/10.1093/gigascience/giab008 | https://www.htslib.org/doc/tabix.html |
| Python library phaser (requires python 3.7) | Castel et al.116 | https://github.com/secastel/phaser |
| WASP v0.3.4 | van de Geijn et al.117 | https://github.com/bmvdgeijn/WASP |
| SnpEff (requires java 1.11.0) | https://pcingola.github.io/SnpEff/adds/SnpEff_paper.pdf | https://pcingola.github.io/SnpEff/ |
| Local ancestry inference R pipeline | Martin et al.118 | https://github.com/armartin/ancestry_pipeline |
| QTLtools v1.3.1 | Delaneau et al.119 | https://qtltools.github.io/qtltools/ |
| R package mixqtl v0.2 | Liang et al.24 | https://github.com/hakyimlab/mixqtl |
| R package coloc v5.1.1 | Wallace et al.120 | https://github.com/chr1swallace/coloc |
| SMR v1.03 | Zhu et al.40 | https://yanglab.westlake.edu.cn/software/smr/ |
| paintor v3.0 | Kichaev et al.121 | https://github.com/gkichaev/PAINTOR_V3.0 |
| R package tidyverse v1.3.1 | https://cran.r-project.org/ | |
| R package dplyr v1.0.7 | https://cran.r-project.org/ | |
| R package data.table v1.14.2 | https://cran.r-project.org/ | |
| R package ggplot2 v3.4.0 | https://cran.r-project.org/ | |
| R package susie v0.11.92 | https://cran.r-project.org/ | |
| R package BiocManager v1.30.6 | https://cran.r-project.org/ | |
| R package devtools v2.4.3 | https://cran.r-project.org/ | |
| R package reshape2 v1.4.4 | https://www.jstatsoft.org/article/view/v021i12 | https://cran.r-project.org/ |
| R package ggrepel v0.9.2 | https://cran.r-project.org/ | |
| R package VennDiagram v1.7.3 | https://cran.r-project.org/ | |
| R package UpSetR v1.4.0 | https://cran.r-project.org/ | |
| R package circlize v0.4.15 | Gu et al.122 | https://cran.r-project.org/ |
| R package GetoptLong v1.0.5 | https://cran.r-project.org/ | |
| R package RColorBrewer v1.1-3 | https://cran.r-project.org/ | |
| R package CMplot v4.2.0 | Yin et al.123 | https://cran.r-project.org/ |
| R package extrafont v0.19 | https://cran.r-project.org/ | |
| R package ComplexHeatmap v2.14.0 | Gu et al.124 | https://github.com/jokergoo/ComplexHeatmap |
| R package peer v1.0 | Stegle et al.125 | https://github.com/PMBio/peer |
| LeafCutter v1.0 | Yang et al.126 | https://github.com/davidaknowles/leafcutter |
| RFMix v2.0 | Maples et al.127 | https://github.com/slowkoni/rfmix |
| Plink v1.9 | Chang et al.128 | https://www.cog-genomics.org/plink/ |
| Custom QTL scripts | This paper | GitHub: https://github.com/MillerLab-CPHG/CAD_QTL and zenodo: https://doi.org/10.5281/zenodo.10095581 |
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