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

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 haplotype association analyses, with unadjusted p-values. Details on these files can be found in the dataset readme and the Methods section of the associated publication.

• 2014 to 2023

• 2024

• Chitre, Apurva S.
• NIDA Center for GWAS in Outbred Rats
• Okamoto, Faith

• Palmer, Abraham A.

Details of how these files were produced may be found in the dataset readme and the Methods section of the associated publication. Software and package versions may be found in the Reagent Table within the associated publication’s Supplementary Files.

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

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
• Palmer, Abraham A. (2023). Heterogeneous Stock (HS) Rat Genotypes, Version 3. In Genotype Data from: NIDA Center for GWAS in Outbred Rats. UC San Diego Library Digital Collections. https://doi.org/10.6075/J00G3KBX
• RatGTex portal: https://ratgtex.org/download/study-data/

Software

• Code for replication: https://doi.org/10.5281/zenodo.11493119

Previous version

• 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

Other resource

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

Creative Commons Attribution 4.0 International Public License

• UC Regents

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.

Research Data Curation Program, UC San Diego, La Jolla, 92093-0175 (https://lib.ucsd.edu/rdcp)

2024-08-23