| Biological Samples |
|
|
| Labrador retrievers whole blood samples |
UC Davis |
N/A |
| Labrador retrievers whole blood samples |
NHGRI |
N/A |
| Critical Commercial Assays |
|
|
| Kapa HTP Library Prep Illumina |
Roche |
KK8234 |
| SeqCap Adapter kit A |
Roche |
7141530001 |
| SeqCap Adapter kit B |
Roche |
7141548001 |
| SeqCap Epi Developer S |
Roche |
7139071001 |
| SeqCap Epi Developer Reagent |
Roche |
6684335001 |
| SeqCap EZ HE-Oligo Kit A |
Roche |
6777287001 |
| SeqCap EZ HE-Oligo Kit B |
Roche |
6777317001 |
| VK SeqCap Epi Reagent Kit plus |
Roche |
7185723001 |
| Seqcap EZ Pure Capture Bead Kit |
Roche |
6977952001 |
| Zymo EZ DNA methylation |
Zymo |
11-334 |
| Kapa Library qPCR quantification |
Roche |
KK4824 |
| Bioanalyzer (DNA 1000) |
Agilent |
5067-1504 |
| Bionalyzer machine |
Agilent |
2938C |
| Kapa HiFi HotStart Uracil Polymerase |
Roche |
KK2801 |
| Covaris microTUBES |
Covaris |
520166 |
| Ampure beads |
Beckman Coulter |
A63881 |
| HiSeq 4000 Reagent kit |
Illumina |
PE-410-1001 |
| Deposited Data |
|
|
| Raw and analyzed data |
This paper |
GEO: GSE146920
|
| Code and associated files |
This paper |
https://doi.org/10.5281/zenodo.3864683 |
| Dog genome (CanFam 3.1) |
Yates et al., 2016 |
http://dec2017.archive.ensembl.org/ |
| Mouse genome (mm10) |
Yates et al., 2016 |
http://dec2017.archive.ensembl.org/ |
| Human genome (hg19) |
Yates et al., 2016 |
http://dec2017.archive.ensembl.org/ |
| CpG Islands & repeat regions |
Rosenbloom et al., 2015 |
https://hgdownload.soe.ucsc.edu/downloads.html |
| Gene & ortholog annotations |
Vilella et al., 2009 |
http://dec2017.archive.ensembl.org/ |
| Mouse RRBS data |
Petkovich et al., 2017 |
GEO: GSE80672
|
| Human (children) 450K array |
Alisch et al., 2012 |
GEO: GSE36054
|
| Human (adults) 450K array. |
Hannum et al., 2013 |
GEO: GSE40279
|
| Dog and wolf RRBS |
Thompson et al., 2017 |
SRA: SRP065319 |
| Gene Ontology |
Ashburner et al., 2000 |
http://geneontology.org/docs/download-ontology/ |
| Software and Algorithms |
|
|
| LiftOver |
Rosenbloom et al., 2015 |
http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads |
| FASTQC |
N/A |
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| TrimGalore (v0.4.5) |
N/A |
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| Bismark (v0.14.3) |
Krueger and Andrews, 2011 |
http://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| MethylDackel |
N/A |
https://github.com/dpryan79/MethylDackel |
| Picard Tools (v1.141) |
N/A |
https://broadinstitute.github.io/picard/ |
| SAMtools |
Li et al., 2009 |
http://www.htslib.org/ |
| BEDtools (v2.25.0) |
Quinlan and Hall, 2010 |
https://bedtools.readthedocs.io/en/latest/ |
| fancyimpute |
N/A |
https://pypi.org/project/fancyimpute/ |
| Minfi (R) |
Aryee et al., 2014 |
https://bioconductor.org/packages/release/bioc/html/minfi.html |
| Impute (R) |
Hastie et al., 2020 |
https://www.bioconductor.org/packages/release/bioc/html/impute.html |
| Modified beta-mixture quantile dilation (BMIQ, R) |
Horvath, 2013; Teschendorff et al., 2013
|
PMID: 24138928; Additional File 24 |
| LOLA (R) |
Sheffield and Bock, 2016 |
https://bioconductor.org/packages/release/bioc/html/LOLA.html |
| preprocessCore (R) |
Bolstad, 2013 |
http://bioconductor.org/packages/release/bioc/html/preprocessCore.html |
| statsmodel (v0.8.0 Python) |
Perktold et al. |
http://www.statsmodels.org/stable/index.html |
| SciPy (v1.1.1 Python) |
Virtanen et al., 2020 |
https://www.scipy.org/ |
| scikit-learn (v0.19.2 Python) |
Pedregosa et al., 2011 |
https://scikit-learn.org/stable/ |
| Cytoscape (v3.7) |
Shannon et al., 2003 |
https://cytoscape.org/download.html |
| clusterMaker2 |
Shannon et al., 2003 |
http://apps.cytoscape.org/apps/clustermaker2 |
| Enrichment Map |
Merico et al., 2011 |
http://apps.cytoscape.org/apps/enrichmentmap |
