Here we provide access to the data associated with the research papers produced by research projects that use HS rats.
See also: the Center’s genotype data for HS rats at the UC San Diego Library Digital Collection*
Raw Sequence Datasets
| Title | Data type | Scope | Submitted by | Date | Accession | ID | |
|---|---|---|---|---|---|---|---|
| Whole-genome sequence data for 88 outbred heterogeneous stock rats | Raw sequence reads | Deep coverage whole- genome sequenced using short-reads lllumina method | Multispecies | Palmer Lab | 2/13/24 | PRJNA1076141 | 1076141 |
| Whole-genome sequence data for 8 heterogeneous stock rat founders | Raw sequence reads | Deep coverage whole-genome sequenced using short-reads lllumina method | Multispecies | Palmer Lab | 12/5/23 | PRJNA1048943 | 1048943 |
| N/NIH heterogeneous stock (HS) outbred rats, low-coverage whole genome sequencing | Raw sequence reads | Low-coverage whole-genome sequencing | Multispecies | Palmer Lab | 9/29/23 | PRJNA1022514 | 1022514 |
Publication Datasets
| Title | Author | Publication | Publication Year | PubMed PMID | Links |
|---|---|---|---|---|---|
| Genome-Wide Association Study in 3,173 Outbred Rats Identifies Multiple Loci for Body Weight, Adiposity, and Fasting Glucose | Chitre, AS et al. | Obesity | 2020 | 32860487 | Manuscript Dataset |
| Genome-Wide Association Study on Three Behaviors Tested in an Open Field in Heterogeneous Stock Rats Identifies Multiple Loci Implicated in Psychiatric Disorders | Gunturkun, MH et al. | Frontiers in Psychiatry | 2022 | 35237186 | Manuscript |
| The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats | Munro, D et al. | Nucleic Acids Research | 2022 | 36263809 | Manuscript |
| Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks | Wright, SN et al. | Cell Reports | 2023 | 37527041 | Manuscript Dataset |
| Genome-wide association study finds multiple loci associated with intraocular pressure in HS rats | Fowler, S et al. | Frontiers in Genetics | 2023 | 36793389 | Manuscript |
| Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population | Okamoto, F et al. | G3: Genes, Genomes, Genetics | 2024 | 39250761 | Manuscript Datasets Genotypes |
| Genome-wide association study of delay discounting in Heterogeneous Stock rats | Lara, MK et al. | Genes, Brain and Behavior | 2024 | 39119916 | Manuscript |
| Genome-wide association study reveals multiple loci for nociception and opioid consumption behaviors associated with heroin vulnerability in outbred rats | Kuhn, B et al. | Molecular Psychiatry | 2025 | 40000848 | Manuscript Genotypes |
| A Cost-effective, High-throughput, Highly Accurate Genotyping Method for Outbred Populations | Chen, D et al. | G3: Genes, Genomes, Genetics | 2025 | 39670731 | Manuscript |
| Genetic Loci Influencing Cue‐Reactivity in Heterogeneous Stock Rats | King, CP et al. | Genes, Brain and Behavior | 2025 | 40049657 | Manuscript |
Project Datasets
| Project Number | Project Title | Project Dates | Phenotypes | Omics Data | Sample Size |
|---|---|---|---|---|---|
| P50DA037844, Project 1 (Years 1-5) | Genetic Studies of Incentive Salience | 2014-2019 | Cocaine Contextual Conditioning; Novelty Seeking; Pavlovian Conditioned Approach | 1625 | |
| P50DA037844, Project 1 (Years 6-10) | Neurogenetic Substrates of Cocaine Addiction | 2019-2024 | Intermittent Access to Cocaine | RNA-Seq | 1286 + 149 |
| P50DA037844, Project 2 | Socially-acquired nicotine self-administration | 2019-2024 | Open Field Novel Object Interaction Test; Nicotine Self-Administration; Progressive Ratio Testing | 4487 | |
| P50DA037844, Project 3 (Years 1-5) (Years 6-10) | Association between behavioral regulation and cocaine cue preference | 2014-2024 | Locomotor Response; Delay Discounting; Light Reinforcement; Locomotor Activity; Reaction Time; Social Reinforcement; Enriched Environment; Pavlovian Conditioned Approach | 1181 + 1726 | |
| R01AR070879 | Identification of Genes Regulating Bone Matrix Composition and Quality | 2016-2021 | Bone Density | 530 | |
| U01DA043799 | Identification of Genetic Variants that Contribute to Compulsive Cocaine Intake in Rats | 2017-2027 | Addiction Index; Aggression Behavior; Defensive Behavior; Behavior Stability; Cocaine Intake | Goal: 1000 Current: 882 |
|
| U01DA044468 | Genomic analysis of avoidance learning in addiction | 2018-2023 | Avoidance Learning | RNA-Seq | 1172 |
| U01DA046077 | Genetic Features of Delay Discounting in an HS Rat Model | 2018-2023 | Delay Discounting; Impulsivity; Five-Choice Serial-Reaction Time Task | RNA-Seq | 650 |
| U01DA045300 | Genetic Basis of Opioid Dependence Vulnerablility | 2018-2023 2025-2030 (Renewal) | Self-Administration; Drug-Seeking | RNA-Seq | Goal: 1000 Current: 523 + 608 |
| U01DA044451 | Use of Next-Gen Sequencing to Identify Genetic Variants that Influence compulsive Oxycodone Intake in Outbred Rats | 2018-2028 | Oxycodone Infusions; Reward Intake; Tail Immersion; Lever Presses | Goal: 1000 Current: 619 |
|
| U01DA050239 | Single-cell resolution analysis of chromatin accessibility and gene expression | 2020-2025 | RNA-seq; ATAC-seq; H3K27Ac; PLAC-seq | 96 | |
| U01DA051972 | Decoding the grammar of transcriptional enhancers regulating different stages of opioid use disorder | 2020-2025 | RNA-Seq | ||
| U01DA051234 | Characterization of Tandem Repeat and Structural Variants Contributing to Addictive Behaviors in Mice and Rats | 2021-2026 | PacBio and ONT | 88 HS rats; 8 founders |
*Items in the UC San Diego Library Digital Collections are available from the UC San Diego Library and are intended to support research, teaching, and private study under fair use.
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CONTACT
Abraham Palmer, PhD : aap@ucsd.edu
Oksana Polesskaya, PhD : opolesskaya@ucsd.edu
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