Okamoto, Faith; Chitre, Apurva S.; Sanches, Thiago M.; Chen, Denghui; Munro, Daniel; Polesskaya, Oksana (2023). Data from: Y and MT Chromosomes in the HS Rat Population (pre-peer review). In The Center for GWAS in Outbred Rats Database (C-GORD). UC San Diego Library Digital Collections. https://doi.org/10.6075/J0M61KFB

The data in this object comes from the publication titled “Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population”, authored by Okamoto et al. The majority of the object is dedicated to the source data analyzed to produce figures and tables throughout the publication. However, this object also contains final results of all association analyses, with unadjusted p-values. Details on these files can be found in the dataset readme and the Methods section of the association publication.

• 2014 to 2023

• 2023

• Chen, Denghui
• Chitre, Apurva S.
• Munro, Daniel
• Okamoto, Faith
• Polesskaya, Oksana
• Sanches, Thiago M.

• Palmer, Abraham A.

Data collection and analysis was funded by P50 DA037844.

• Rattus norvegicus

• Bioinformatics and computational biology
• Biological sciences
• Differential expression
• Haplotype
• Heterogeneous stock (HS) rats
• Low-coverage sequencing
• Mitochondrial chromosome
• Outbred
• PheWAS
• Rat
• RNA-Seq
• Y chromosome

• data
• text

• English

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

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

Identifier: Daniel Munro: https://orcid.org/0000-0002-0724-218X

Identifier: Denghui Chen: https://orcid.org/0000-0002-6541-3418

Identifier: Faith Okamoto: https://orcid.org/0009-0007-4163-6928

Identifier: Oksana Polesskaya: https://orcid.org/0000-0003-3024-114X

Identifier: Thiago M. Sanches: https://orcid.org/0000-0001-6962-9569

Doi: https://doi.org/10.6075/J0M61KFB

Primary associated publication

• Okamoto F, Chitre AS, Sanches TM, Chen D, Munro D, NIDA Center for GWAS in Outbred Rats, Polesskaya O, Palmer AA 2023. Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population. bioRxiv. https://doi.org/10.1101/2023.11.29.566473

Source data

• N/NIH heterogeneous stock (HS) outbred rats, low-coverage whole genome sequencing, Sequence Read Archive, accession PRJNA1022514. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1022514
• RatGTex portal: https://ratgtex.org/download/study-data/

Software

• Code for replication: https://github.com/Palmer-Lab-UCSD/y-mt-code-for-okamoto-et-al
• Faith-Okamoto-Palmer-lab. (2023). Palmer-Lab-UCSD/y-mt-code-for-okamoto-et-al: Code for preprint (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.10234038

Newer version

• Okamoto, Faith; Chitre, Apurva S.; NIDA Center for GWAS in Outbred Rats; Palmer, Abraham A. (2024). Data from: Y and MT Chromosomes in the Heterogeneous Stock Rat Population. In The Center for GWAS in Outbred Rats Database (C-GORD). UC San Diego Library Digital Collections. https://doi.org/10.6075/J0VX0GQQ

Reference

• Chen D, Chitre A, Cheng R, Peng B, Polesskaya O, Palmer A. 2023 Oct 20. Palmer Lab Heterogeneous Stock Rats Genotyping Pipeline. https://zenodo.org/records/10002191. [accessed 2023 Nov 29]. https://doi.org/10.5281/zenodo.10002191
• Chen D, Chitre A, Cheng R, Peng B, Polesskaya O, Palmer A. 2023 Oct 20. Palmer Lab High Coverage WGS DeepVariant Genotyping Pipeline. https://zenodo.org/records/10027133. [accessed 2023 Nov 28]. https://doi.org/10.5281/zenodo.10027133
• Gileta AF, Gao J, Chitre AS, Bimschleger HV, St. Pierre CL, Gopalakrishnan S, Palmer AA. 2020. Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats. G3 (Bethesda). 10(7):2195–2205. https://doi.org/10.1534/g3.120.401325

Other resource

• NIDA Center for GWAS in Outbred Rats (ratgenes.org)

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• UC Regents

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2024-06-14