Data Resources

The Center maintains foundational rat omics datasets that any researcher can use on day one of a project, as a learning tool for quantitative genetics concepts, as a reference for developing functional hypotheses, or as a complementary resource to combine with your own data.

Foundational datasets

These datasets were produced by the rat omics community, including many from this Center and its cores. Together they describe the reference assemblies, genome sequence, chromatin conformation, transcriptome, and proteome of the NIH Heterogeneous Stock (HS) and the Hybrid Rat Diversity Panel (HRDP), and of the inbred and recombinant inbred strains used to study them. They support QTL mapping, expression quantitative trait analysis, and network analysis across genetically diverse animals.

• Reference genomes. The GRCr8 and mRatBN7.2 rat reference assemblies, the SHRSP telomere-to-telomere assembly, and a pangenome built from 8 inbred strain genomes. These set the coordinate system and the strain-level sequence context for the other datasets here.

• Whole-genome sequence. Illumina short-read and 10X Genomics linked-read sequence for 163 rats from 88 strains and 32 substrains, about 80% of the HRDP, with PacBio HiFi and CLR long reads, Oxford Nanopore reads, and Hi-C for assembly and phasing. Joint variant and structural variant call sets accompany the assemblies.

• Chromatin conformation. Hi-C from frontal cortex of nine inbred strains and one F1 hybrid, used for assembly scaffolding and to examine functional loops in brain.

• Transcriptome and regulatory data. Brain and liver transcriptome data with eQTL, network, and promoter tools, plus transcription start sites and alternative polyadenylation sites from nucleus accumbens and prefrontal cortex.

• Proteomics. TMT-based quantitative brain proteomics across the HXB/BXH panel, with cis-pQTL results.

• Nexus Panel multi-omics (in progress). A 10-strain inbred panel designed to capture most of the genetic variation in the HS and HRDP (see the Nexus Rat Panel page). The SMART core is generating whole-genome CpG methylation, direct RNA sequencing, and long-read snRNA-seq from nucleus accumbens, medial prefrontal cortex, and amygdala in both sexes, and the SAM core is generating a matching proteomics dataset.

Where to get the data

The following resources from the rat genetics community are available now. They cover the populations the Center works with. Expand a data type to see the datasets, their access links, and the associated publication.

Programmatic access

Four of the resources above serve their data through a REST API, so datasets can be retrieved without using a web interface.

PhenoGen

PhenoGen provides an API for retrieving datasets and expression, genotype, and phenotype files, and an R package that wraps the API so data can be pulled directly into R. File downloads on the PhenoGen downloads page are temporarily unavailable while the site is updated, and the API provides access in the meantime.

• Production API endpoint. rest.phenogen.org

• API documentation. rest-doc.phenogen.org

• PhenoGenRESTR R package. github.com/TabakoffLab/PhenoGenRESTR

• Download and dataset listing. phenogen.org/web/sysbio/resources.html

GeneNetwork

The GeneNetwork REST API returns species and group lists, genotypes in BIMBAM, R/qtl2, or geno format, dataset and trait metadata, sample data as CSV or JSON, mapping results from GEMMA and R/qtl, and trait correlations. The GNapi R package wraps the same endpoints, and GeneNetwork3 is the backend that adds newer endpoints.

• API base URL. genenetwork.org/api/v_pre1/

• API reference. GN2 REST API documentation

• GNapi R package. github.com/rqtl/GNapi

• GeneNetwork3 backend. github.com/genenetwork/genenetwork3

RatGTEx

RatGTEx serves its v4 release through a REST API. Queries return tissue metadata with sample counts and eGene counts, gene and variant metadata, exon annotations, per-sample expression in TPM, the top expressed genes in a tissue, and single-tissue, conditionally independent, and dynamic cis-eQTL and cis-xQTL results across RNA modalities. The v4 release uses the GRCr8 assembly, and earlier releases remain available from the download page.

• API base URL. ratgtex.org/api/v4/

• API reference and OpenAPI specification. ratgtex.org/about/api/

• Data downloads. ratgtex.org/download/

Rat Genome Database

The Rat Genome Database (RGD) REST API returns rat genes, QTLs, strains, variants, phenotypes, and ontology annotations. The Swagger UI documents each endpoint and runs queries in the browser.

• API base URL. rest.rgd.mcw.edu/rgdws/

• API reference (Swagger UI). rest.rgd.mcw.edu/rgdws/swagger-ui/index.html

FAIR access

The Admin core serves as the Center's data clearinghouse. All OSGA-generated data and metadata are deposited in appropriate public repositories, including single-cell omics data in the Neuroscience Multi-Omics (NeMO) Archive, and are released under FAIR principles. Datasets and access points are cataloged on this page as they are released.