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See the About page for processing, data format, and RatGTEx version number specifications. File names include the version number, and files that include genomic coordinates also include the genome build for clarity, even though only one genome build is used for each version.

Gene info

Gene expression

Median TPM per gene per tissue Used for heatmap visualizations

log2(readcount+1) Used to compute allelic fold change

Adipose • BLA • Brain • Eye • IC • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg

TPM (transcripts per million) Relative abundance of transcripts

Adipose • BLA • Brain • Eye • IC • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg


All RNA phenotypes

The TPM files above are the same as the unnormalized expression files below.

Unnormalized TPM, ratios, etc.
Expression Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Isoform ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Intron excision ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative TSS usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative polyA usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
RNA stability Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg

Normalized Quantile-normalized and inverse-normal-transformed
Expression Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Isoform ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Intron excision ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative TSS usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative polyA usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
RNA stability Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg

eQTLs

Conditionally independent cis-eQTLs
A table of cis-eQTLs from all tissues.

Top association per gene
A table of the strongest variant-gene association per gene per tissue, even if not significant. A q-value threshold of 0.05 was used to determine significant eQTLs.

trans-eQTLs
All SNP-gene associations genome-wide with TSS distance > 5 Mb and with an arbitrary cutoff of p < 1e-5. No significance testing was performed.

Adipose • BLA • Brain • Eye • IC • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg


All xQTLs

Conditionally independent cis-xQTLs for all tissues
Cross-modality mapped (conditionally independent across modalities per gene per tissue)
Each modality mapped separately: expression • isoforms • splicing • alt_TSS • alt_polyA • stability

All significant cis-xQTL variant-phenotype pairs
Expression Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Isoform ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Intron excision ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative TSS usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative polyA usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
RNA stability Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg

Top association per gene for all tissues
A table of the strongest variant-gene association per gene per tissue, even if not significant. A q-value threshold of 0.05 was used to determine significant xQTLs.
Cross-modality mapped
Each modality mapped separately: expression • isoforms • splicing • alt_TSS • alt_polyA • stability


Other info

Genotypes

Rat info (all tissues)

Sample info (all tissues)

Rat IDs The final QC-filtered sample sets used for eQTL mapping

Adipose • BLA • Brain • Eye • IC • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg

RNA-Seq FASTQ file lists with corresponding rat IDs
Each line includes one FASTQ path for single-end reads, or two FASTQ paths for paired-end reads, followed by the rat ID. FASTQ maps can include a mix of single-end and paired-end rows. These files may include mappings to samples that were filtered out during QC, so use the rat ID lists above to get the final sample sets.

Adipose • BLA • Brain • Eye • IC • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg

Covariates used for xQTL mapping
Expression Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Isoform ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Intron excision ratio Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative TSS usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
Alternative polyA usage Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg
RNA stability Adipose BLA Brain Eye IC IL LHb Liver NAcc OFC PL pVTA RMTg

API

Different types of data used for visualizations, including expression, eQTLs, and reference annotations, can be accessed via API. See the API documentation for details.


Raw data

RNA-Seq reads from each originating study are available in NCBI's sequence read archive (SRA) and can be accessed from the following GEO accessions. Some of these are SuperSeries accessions that group multiple tissue datasets, each of which has its own Series accession that can be found in the SuperSeries entry. Accessions marked private are inaccessible until their originating study is published.

Warning: Sample QC, including relabeling swapped sample IDs, was performed for each data release to ensure consistency with new genotype data. When possible, we marked samples that were removed or relabeled in the GEO metadata, but this may not match the latest version exactly. If using these RNA-seq data alongside genotypes, we recommend testing for genetic variant concordance between RNA-seq and genotypes for correct sample matching.

Tissues GEO accession
IL, LHb, NAcc1, OFC, PL1 GSE173141
Adipose GSE196572
Liver GSE200453
Eye GSE201236
Brain GSE319591
BLA, NAcc2, PL2 GSE325289 (private)
NAcc3, PL3, pVTA1 GSE325483
IC, NAcc4, pVTA2 GSE325599 (private)
RMTg GSE325609

Original study data

Archives of the data files used in the originating studies.