Palmer, Abraham A. (2024). Heterogeneous Stock (HS) Rat Genotypes, Version 4. In Genotype Data from: NIDA Center for GWAS in Outbred Rats. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0X63N54

This collection contains genotype data collected as part of the NIDA Center for GWAS in Outbred rats and more than 10 additional research projects that use N/NIH heterogeneous stock (HS) outbred rats. We obtain genotypes for DNA samples derived from rats that are phenotyped by different research projects. We use these genotypes to perform genome wide association studies (GWAS) and a number of related analyses. Data in this release contains genotypes for 17,812 N/NIH heterogeneous stock (HS) outbred rats from the breeding colonies MCW: NMcwi:HS RRID:RGD_2314009, and WFU: NMcwiWFsm:HS RRID:RGD_13673907, the University of California San Diego: RRID: RGD_155269102, the University of Tennessee Health Sciences Center, or Oregon Health and Sciences University.

We release updated data every 2-3 months, and provide detailed information on our genotyping pipeline in the Readme file associated with the object.

• Date of data collection: 2014 to 2023. Date of version: 2023-12-15.

• 2024

• Palmer, Abraham A.

• Palmer, Abraham A.

All software versions used to generate the data in this object are noted below and in the Methods section of the associated publication:

fastx_toolkit 0.0.14
cutadapt 4.1
fgbio 1.3.0
bbDuk 38.94
BWA 0.7.17
samtools 1.14
picard 2.25.7
STITCH 1.6.6
GATK 4.2.0
bcftools 1.14
PLINK 1.9
Python 3.10

Demultiplexing was performed using fastx_toolkit and fgbio. Barcode, adapter, and quality trimming was performed using cutadapt and bbDuk. Reads were aligned to the Rattus norvegicus genome assembly mRatBN7.2 using BWA. Read mapping was quantified using samtools. SNP genotypes were imputed using STITCH and a reference panel of consensus variants identified from eight HS rat founder strains. Reference panel SNPs were called using GATK. Variants were filtered using bcftools. Quality control was conducted using Python.

NIDA center for genetic studies of drug abuse in outbred rats (P50DA037844).

• Rattus norvegicus

• Algorithm: Unsupervised learning
• Biological sciences
• Genetics
• Genotyping-by-sequencing (GBS)
• Heterogeneous stock (HS) rats
• Imputation
• Low-Coverage Whole Genome Sequencing (lc-WGS)
• Norway rat
• Rat
• Task: Clustering

• data
• text

• English

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

Doi: https://doi.org/10.6075/J0X63N54

Software

• Chen, D., Chitre, A., Cheng, R., Peng, B., Polesskaya, O., & Palmer, A. (2023). Palmer Lab Heterogeneous Stock Rats Genotyping Pipeline (v3.0.0). Zenodo. https://doi.org/10.5281/zenodo.10002191

Related data

• Rat Genome Database -- Strain: McwiWfsmAap:HS, RRID:RGD_155269102 https://scicrunch.org/resolver/RGD_155269102
• Rat Genome Database -- Strain: NMcwi:HS, RRID:RGD_2314009 https://scicrunch.org/resolver/RGD_2314009
• Rat Genome Database -- Strain: NMcwiWfsm:HS, RRID:RGD_13673907 https://scicrunch.org/resolver/RGD_13673907
• The data have been deposited with links to BioProject accession number PRJNA487943 in the NCBI BioProject database: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA487943/

Reference

• Alexander F Gileta, Jianjun Gao, Apurva S Chitre, Hannah V Bimschleger, Celine L St. Pierre, Shyam Gopalakrishnan, Abraham A Palmer, Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats, G3 Genes | Genomes | Genetics, Volume 10, Issue 7, 1 July 2020, Pages 2195–2205. https://doi.org/10.1534/g3.120.401325
• Ramdas, S., Ozel, A.B., Treutelaar, M.K. et al. Extended regions of suspected mis-assembly in the rat reference genome. Sci Data 6, 39 (2019). https://doi.org/10.1038/s41597-019-0041-6

Other resource

• Rat Genes (ratgenes.org)

Creative Commons Attribution 4.0 International Public License

• UC Regents

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2024-07-10