Please cite as: 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. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0K074G9 Corresponding author: Abraham A. Palmer aap@ucsd.edu Primary associated publication: Chitre, A. S., Hebda-Bauer, E. K., Blandino, P., Bimschleger, H., Nguyen, K.-M., Maras, P., Li, F., Ozel, A. B., Pan, Y., Polesskaya, O., Cheng, R., Flagel, S. B., Watson, S. J., Li, J., Akil, H., & Palmer, A. A. (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 Description of contents: 1. phenotype_data.zip This zipped folder contains unprocessed and processed phenotype data: raw_phenotypes_N539.csv --This file contains the raw phenotypes. processed_phenotypes_N539.csv --This file contains the residuals (processed phenotype data) used for GWAS. 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 --This file contains phenotype descriptions. 2. genotype_data.zip This zipped folder contains the genotypes for F0, F2 as well as the Genetic Relatedness Matrix (GRM) for the F2 rats. F0_genotypes.zip --This zipped folder contains the genotype data for the F0 rats in VCF file format. F2_genotypes_VCF.zip --This zipped folder contains the genotype data for the F2 rats in VCF file format. F2_genotypes_PLINK.zip --This zipped folder contains the genotype data for the F2 rats in PLINK file format. --VCF format: Contains meta-information lines, a header line, and then data lines each containing information about the SNPs. --PLINK binary format: .bed is the PLINK binary biallelic genotype table. This is the primary representation of genotype calls at biallelic variants. The .bed file is accompanied by .bim (Variant information) and .fam (Sample information) files. The compressed VCF files can be handled using bcftools (https://samtools.github.io/bcftools/bcftools.html) and vcftools (https://vcftools.github.io/index.html). F2_GRM.zip --This zipped folder contains the Genetic Relatedness Matrix (GRM) for the F2 rats produced using GCTA. gcta v1.93.2 beta was used to produce the GRM using the following command: gcta --bfile genotype --autosome-num 20 --autosome --thread-num 1 --make-grm-bin --out F2 F2.grm.bin (binary file which contains the lower triangle elements of the GRM). F2.grm.N.bin (binary file which contains the number of SNPs used to calculate the GRM). F2.grm.id (no header line; columns are individual IDs). 3. gwas_results.zip This zipped folder contains the results from the GWAS analysis (.loco.mlma files) GWAS analysis employed a linear mixed model and genetic relatedness matrices (GRM) to account for relatedness and the Leave One Chromosome Out (LOCO) method to avoid proximal contamination. columns are chromosome, SNP, physical position, reference allele (the coded effect allele), the other allele, frequency of the reference allele, SNP effect, standard error and p-value 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 License: Creative Commons Attribution 4.0 International Public License