Data from: Y and MT Chromosomes in the HS Rat Population (pre-peer review)
Readme
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Description | Detailed descriptions of all files in this dataset. |
Sample metadata
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Description | CSV file with metadata on all modern HS rats used in this study: RFID, sex, library preparation method, and date of birth. |
Raw genotypes
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Description | VCF files with Y and MT genotypes for all samples used in this study. A copy of the MT reference sequence is included. |
Genetic relationship matrix
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Description | Files representing a GRM constructed from autosomal SNPs for all modern HS rats. |
GWAS expression phenotypes
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Description | Three CSV files, one with all (pre-processed) complex traits originally used for GWAS, for all phenotyped modern rats, and another matching trait names to their original projects. Trait names are anonymized to respect unpublished collaborations. An additional file has kidney count at birth for all rats where that is known. |
Gene expression phenotypes
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Description | DE gene expression tables from RatGTex for all tissues datasets used in this study. Expression values are “log2” read counts without any normalization applied. |
Sequencing depth along MT
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Description | CSV file with read depth at each position along the MT reference for all modern HS rats used in this study. |
Association test results
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Description | CSV files with results of all association tests. Included are metadata about the test conducted, along with p-values, both adjusted and unadjusted for multiple test correction. |
- Collection
- Cite This Work
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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
- Description
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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.
- Creation Date
- 2014 to 2023
- Date Issued
- 2023
- Authors
- Principal Investigator
- Funding
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Data collection and analysis was funded by P50 DA037844.
- Scientific Name
- Topics
Formats
View formats within this collection
- Language
- English
- Identifier
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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
- Related Resources
- 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
- 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/
- 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
- 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
- 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
Primary associated publication
Source data
Software
Newer version
Reference
Other resource
- License
-
Creative Commons Attribution 4.0 International Public License
- Rights Holder
- UC Regents
- Copyright
-
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
2024-06-14