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Data from: Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

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Data from: Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies

About this collection

Extent

1 digital object.

Cite This Work

Gileta, Alexander F.; Fitzpatrick, Christopher J.; Chitre, Apurva S.; St. Pierre, Celine L.; Joyce, Elizabeth V.; Maguire, Rachael J.; McLeod, Africa M.; Gonzales, Natalia M.; Williams, April E.; Morrow, Jonathan D.; Robinson, Terry E.; Flagel, Shelly B.; Palmer, Abraham A. (2022). Data from: Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0XS5V8K

Description

The data in this collection comes from the publication titled “Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies”, authored by Gileta et al. The majority of the collection is dedicated to the supplementary information (figures, tables, files) presented throughout the publication. However, this collection also contains additional information beyond what is presented, including (1) a VCF file containing all raw SNP calls with dosage data in the original set of 4,625 Sprague Dawley rats, (2) filtered variants in BIM/BED/FAM format for each of the seven Sprague Dawley genetic subgroupings, and (3) summary files for the GWAS results for all 55 metric x training day combinations for all individual subgroups and their meta-analyses. Details on how these files were generated can all be found in the Methods section of the associated publication.

Creation Date
  • 2011 to 2021
Date Issued
  • 2022
Authors
Principal Investigator
Co Principal Investigators
Researchers
Data Manager
Advisor
Contributors
Technical Details

All relevant tools and software used to generate the data in this collection are noted below and in the Methods section of the associated publication.

FASTQ Processing: Cutadapt v1.9.1, FASTX Clipper/Trimmer/Quality Trimmer tools v0.0.13,
Alignment: Burrows-Wheeler Aligner v0.7.5a, samtools-1.3, GATK IndelRealginer v3.5
Variant Calling: ANGSD v0.911
Imputation: Beagle4.1 Feb 22nd 2016 release
VCF Filtering: plink-1.90
GWAS: GEMMA v0.97
Meta-analysis: MR-MEGA ver.0.2

Funding

This work was funded by the National Institute of Drug Addiction (NIDA; https://www.drugabuse.gov/) through R21 DA036672 (AAP; TER; SBF), P50 DA037844 (AAP; TER; SBF), and F31 DA039638-02 (AFG), as well as training grant T32 GM007197 (AFG) from the National Institute of General Medical Sciences (NIGMS; https://www.nigms.nih.gov/).

Corporate Names
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Format

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Language
  • English
Identifier

Abraham A. Palmer: https://orcid.org/0000-0003-3634-0747

Africa M. McLeod: https://orcid.org/0000-0002-1122-3715

Alexander F. Gileta: https://orcid.org/0000-0002-7793-8043

April E. Williams: https://orcid.org/0000-0001-9281-8528

Apurva S. Chitre: https://orcid.org/0000-0003-1709-9214

Celine L. St. Pierre: https://orcid.org/0000-0001-5465-6601

Elizabeth V. Joyce: https://orcid.org/0000-0002-8133-2298

Jonathan D. Morrow: https://orcid.org/0000-0002-3530-4544

Natalia M. Gonzales: https://orcid.org/0000-0001-5289-0410

Rachael J. Maguire: https://orcid.org/0000-0001-5712-3616

Shelly B. Flagel: https://orcid.org/0000-0002-7309-9908

Terry E. Robinson: https://orcid.org/0000-0001-7861-3737

Related Resources

    Primary associated publication

    • Alexander F. Gileta, Christopher J. Fitzpatrick, Apurva S. Chitre, Celine L. St. Pierre, Elizabeth V. Joyce, Rachael J. Maguire, Africa M. McLeod, Natalia M. Gonzales, April E.Williams, Jonathan D. Morrow, Terry E. Robinson, Shelly B. Flagel, Abraham A. Palmer (2021). Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies. bioRxiv. https://doi.org/10.1101/412924

    Source data