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Data from: Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits

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Readme

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  • 4.09 KB
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  • Plain text
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Phenotype data

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  • 44.8 KB
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  • ZIP Format
Description

Contains unprocessed and processed phenotype data. Residuals (processed phenotype data) used for GWAS were produced using the following approach: We quantile normalized the phenotypes prior to GWAS. To account for sex differences, we performed the quantile normalizations separately for males and females and then pooled the resulting values. We examined the effect of age on each phenotype using linear regression and found that age did not explain a significant proportion of variance. data_dictionary.csv contains phenotype descriptions.

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Genotype data and Genetic Relatedness Matrix (GRM)

File Size
  • 1.1 GB
File Format
  • ZIP Format
Description

This zipped folder contains the genotypes for F₀, F₂ as well as the Genetic Relatedness Matrix (GRM) for the F₂ rats.
F0 variant calls: The 10X Genomics Chromium fastq files were aligned using the Lariat aligner to rat reference genome Rnor_6.0 (rn6) from Rat Genome Sequencing Consortium (GCA_000001895.4 GCF_000001895.5). Duplicate marking after alignment was done using Picard’s MarkDuplicates tool. Variant calling was performed using bcftools. After variant calling step, we applied SNP filters QUAL >= 30 and F_MISS <= 0.05 to obtain 9.61M biallelic SNPs.

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GWAS results

File Size
  • 780 MB
File Format
  • ZIP Format
Description

This zipped folder contains the results from the GWAS analysis (.loco.mlma files).

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Collection
Cite This Work

Chitre, Apurva S.; Hebda-Bauer, Elaine K.; Blandino, Peter; Bimschleger, Hannah; Nguyen, Khai-Minh; Maras, Pamela M.; Li, Fei; Ozel, A. Bilge; Pan, Yanchao; Polesskaya, Oksana; Cheng, Riyan; Flagel, Shelly B.; Watson, Jr., Stanley J.; Li, Jun; Akil, Huda; Palmer, Abraham A. (2023). Data from: Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits. In Abraham A. Palmer Lab Research Data Collection. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0K074G9

Description

The data in this object comes from the publication titled “Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits”, authored by Chitre et al. The majority of the object is dedicated to the phenotypic and genetic data presented throughout the publication. However, this object also contains additional information beyond what is presented, including (1) a genetic relatedness matrix, (2) Summary files for the GWAS results for all phenotypes, (3) Trait descriptions. Details on how these files were generated can all be found in the Methods section of the associated publication.

Date Collected
  • 2019 to 2021
Date Issued
  • 2023
Authors
Technical Details

All software versions used to generate the data in this collection are noted below, in the Methods section of the associated publication and the Github repository (https://github.com/ApurvaChitre/GWAS_ExploratoryLocomotion_F2)
-- GWAS: gcta v1.93.2 beta
-- Processing genotype data : PLINK v1.90

The compressed VCF files can be handled using bcftools (https://samtools.github.io/bcftools/bcftools.html) and vcftools (https://vcftools.github.io/index.html).

Funding

This work was supported by the National Institute on Drug Abuse (U01DA043098), Office of Naval Research (ONR) (00014-19-1-2149), The Hope for Depression Research Foundation (HDRF) and the Pritzker Neuropsychiatric Research Consortium.

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Language
  • English
Identifier

Identifier: A. Bilge Ozel: https://orcid.org/0000-0002-1112-4258

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

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

Identifier: Elaine K. Hebda-Bauer: https://orcid.org/0000-0002-0043-3944

Identifier: Hannah Bimschleger: https://orcid.org/0000-0001-6578-7201

Identifier: Huda Akil: https://orcid.org/0000-0003-0623-1056

Identifier: Khai-Minh Nguyen: https://orcid.org/0000-0003-3939-7773

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

Identifier: Riyan Cheng: https://orcid.org/0000-0002-8670-795X

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

Identifier: Stanley J. Watson Jr.: https://orcid.org/0000-0003-4980-5523

Identifier: Yanchao Pan: https://orcid.org/0000-0002-4288-3046

Related Resources

    Primary associated publication

    • Apurva S. Chitre, Elaine K. Hebda-Bauer, Peter Blandino, Hannah Bimschleger, Khai-Minh Nguyen, Pamela Maras, Fei Li, A. Bilge Ozel, Oksana Polysskaya, Riyan Cheng, Shelly B. Flagel, Stanley J. Watson Jr., Jun Li, Huda Akil, Abraham A Palmer. Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits. bioRxiv 2022.07.12.499605. https://doi.org/10.1101/2022.07.12.499605

    • Apurva S. Chitre, Elaine K. Hebda-Bauer, Peter Blandino, Hannah Bimschleger, Khai-Minh Nguyen, Pamela Maras, Fei Li, A. Bilge Ozel, Yanchao Pan, Oksana Polesskaya, Riyan Cheng, Shelly B. Flagel, Stanley J. Watson Jr., Jun Li, Huda Akil, Abraham A Palmer. (2023). Genome-Wide Association Study in a Rat Model of Temperament Identifies Multiple Loci for Exploratory Locomotion and Anxiety-Like Traits. Frontiers in Genetics, 13, 1003074. https://doi.org/10.3389/fgene.2022.1003074

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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

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

Last Modified

2023-02-15