Other
| Description | Source / Repository | Persistent ID / URL |
|---|---|---|
| Human embryonic heart tissue | Joint MRC/Wellcome Trust Human Developmental Biology Resource | www.hdbr.org |
| Software and Algorithms: | ||
| Basemount | Illumina | https://basemount.basespace.illumina.com/ |
| FASTQC (v0.11.5) | Andrews, 2010 |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 |
| MultiQC (v1.1) | Ewels et al., 2016 |
http://multiqc.info/ RRID:SCR_014982 |
| Trimmomatic (v.0.36) | RRID:SCR_011848 | |
| Bowtie2 (v2.2.5) | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| PhantomPeakQualTools (v.1.14) | Landt et al., 2012 |
https://code.google.com/p/phantompeakqualtools/ RRID:SCR_005331 |
| HOMER (v4.9) | Heinz et al., 2010 |
http://homer.ucsd.edu/homer/ RRID:SCR_010881 |
| BEDtools (v2.25.0) | Quinlan and Hall, 2010 |
https://github.com/arq5x/bedtools2 RRID:SCR_006646 |
| MACS2 (2.1.1.20160309) | Feng et al., 2012 | https://github.com/taoliu/MACS/ |
| Kent Source Tools (v329) | Kent et al., 2002 | https://github.com/ENCODE-DCC/kentUtils |
| deepTools2 (v2.5.0.1) | Ramírez et al., 2014 | https://github.com/fidelram/deepTools |
| ChromImpute (v1.0.3) | Ernst and Kellis, 2015 | http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/ |
| ChromHMM (v1.12) | Ernst and Kellis, 2012 | http://compbio.mit.edu/ChromHMM/ |
| R Project for Statistical Computing (v3.4.1) | Team, 2017 |
http://www.r-project.org/ RRID:SCR_001905 |
| GREAT (v4.0.4) | McLean et al., 2010 |
http://great.stanford.edu/public/html/splash.php RRID:SCR_005807 |
| DiffBind | Stark and Brown, 2011 | https://doi.org/doi:10.18129/B9.bioc.DiffBind |
| rGREAT | https://doi.org/doi:10.18129/B9.bioc.rGREAT | |
| Homerkit | https://github.com/slowkow/homerkit | |
| Rtsne | https://github.com/jkrijthe/Rtsne | |
| GARFIELD (v2) | Iotchkova et al., 2019 | https://www.ebi.ac.uk/birney-srv/GARFIELD/ |
| GREGOR | RRID:SCR_009165 | |
| GWAS Studies Used: | ||
| GWAS Catalog (retrieved 2019-08-10, All associations v1.0.2) | Welter et al., 2014 |
http://www.ebi.ac.uk/gwas/home RRID:SCR_012745 |
| Systolic Blodd Pressure (2046 Associations) | EFO_0006335 | https://www.ebi.ac.uk/gwas/home |
| Atrial Fibrillation (371 Associations) | EFO_0000275 | https://www.ebi.ac.uk/gwas/home |
| Electrocardiograph Traits and Measures (38 Associations) | EFO_0004327 | https://www.ebi.ac.uk/gwas/home |
| Resting Heart Rate (129 Assocations) | EFO_0005054 | https://www.ebi.ac.uk/gwas/home |
| Congenital Heart Defects (72 Associations) | EFO_0005207, EFO_0005269 | https://www.ebi.ac.uk/gwas/home |
| QT interval (311 Associations) | EFO_0004682 | https://www.ebi.ac.uk/gwas/home |
| QRS (186 Associations) | EFO_0005055, EFO_0007742, | https://www.ebi.ac.uk/gwas/home |
| Coronary Artery Disease (936 Associations) | EFO_0000378 | https://www.ebi.ac.uk/gwas/home |
| Crohns Disease (594 Associations) | EFO_0000384 | https://www.ebi.ac.uk/gwas/home |
| QRS Interval GWAS Summary Statistics (Total SNPs with calculated p-value: 26566045) | Wojcik et al., 2019 | ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/WojcikGL_31217584_GCST008054/WojcikG_PMID_qr s_interval.gz |
| Resting Heart Rate GWAS Summary Statistics (Total SNPs with calculated p-value: 5264922) | Zhu et al., 2019 | ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistic s/ZhuZ_30940143_GCST007609/ZhuZ_30940143_ukbb.bolt_460K_selfRepWhite.rhrmean.assoc.gz |
| Atrial Fibrillation GWAS Summary Statistics (Total SNPs with calculated p-value: 12149979) | Roselli et al., 2018 | https://personal.broadinstitute.org/mvon/AF_HRC_GWAS _ALLv11.zip |
| P-Wave Duration GWAS Summary Statistics (Total SNPs with calculated p-value: 872325) | Christophersen et al., 2017 | ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistic s/ChristophersenIE_28794112_GCST004826/harmonise d/28794112-GCST004826-EFO_0005094build37.f.tsv.gz |
| Systemic lupus erythematous GWAS Summary Statistics (Total SNPs with calculated p-value: 7915251) | Bentham et al., 2015 | ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistic s/BenthamJ_26502338_GCST003156/harmonised/26502 338-GCST003156-EFO_0002690-build37.f.tsv.gz |
| Crohn’s Disease GWAS Summary Statistics (Total SNPs with calculated p-value: 154590) | Liu et al., 2015 | ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistic s/LiuJZ_26192919_GCST003044/CD_trans_ethnic_asso ciation_summ_stats_b37.txt.gz |