Data from: Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies
SD sequencing run summaries
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Description | This Excel file contains the metadata for the sequencing runs we performed on the Sprague Dawley rats. All runs were perform with single-end, 125bp reads on HiSeq2500s. |
Supporting files from Gileta et al. (2021)
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Description | This directory includes all figures, tables, and files noted throughout the publication “Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies”. |
Unfiltered VCF for Sprague Dawley rats
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Description | This variant call file (VCF) contains the rawest form of genotype calls for the full Sprague Dawley rat sample set (~4,625). This VCF was generated from double-digest genotype-by-sequencing and occasional WGS data. |
Filtered VCF & BED/BIM/FAM files for all seven SD subgroups
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Description | This directory contains the filtered variant calls used for the individual subgroup GWAS presented in the publication. The variants are presented here in both VCF and BED/BIM/FAM formats used by plink and other genetic analysis tools. |
SD Pavlovian conditioned approach full GWAS results
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Description | Summary files for the GWAS results for all 55 metric x day combinations for all analyses, individual subgroups and meta-analyses. |
- Collection
- Cite This Work
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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. In Abraham A. Palmer Lab Research Data Collection. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0XS5V8K
- Description
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The data in this object 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 object is dedicated to the supplementary information (figures, tables, files) presented throughout the publication. However, this object 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
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All relevant tools and software used to generate the data in this object 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
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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
- Topics
Format
View formats within this collection
- Language
- English
- Identifier
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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
- 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
- Gileta AF, Fitzpatrick CJ, Chitre AS, St. Pierre CL, Joyce EV, Maguire RJ, et al. (2022) Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies. PLoS Genet 18(5): e1010234. https://doi.org/10.1371/journal.pgen.1010234
- NCBI SRA repository of Sprague Dawley sequencing data and alignments: https://www.ncbi.nlm.nih.gov/sra/PRJNA779552
Primary associated publication
Source data
- License
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Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
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Under copyright (US)
Use: This work is available from the UC San Diego Library. This digital copy of the work is intended to support research, teaching, and private study.
Constraint(s) on Use: This work is protected by the U.S. Copyright Law (Title 17, U.S.C.). Use of this work beyond that allowed by "fair use" or any license applied to this work requires written permission of the copyright holder(s). Responsibility for obtaining permissions and any use and distribution of this work rests exclusively with the user and not the UC San Diego Library. Inquiries can be made to the UC San Diego Library program having custody of the work.
- Digital Object Made Available By
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Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)
- Last Modified
2023-07-13