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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

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

TPM (transcripts per million) Relative abundance of transcripts

BLA • Brain • Eye • IC • IL • LHb • 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	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Isoform ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Intron excision ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative TSS usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative polyA usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
RNA stability	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg

Normalized Quantile-normalized and inverse-normal-transformed

Expression	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Isoform ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Intron excision ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative TSS usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative polyA usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
RNA stability	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg

eQTLs

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

All significant cis-eQTL variant-gene pairs

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

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.

BLA • Brain • Eye • IC • IL • LHb • 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	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Isoform ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Intron excision ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative TSS usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative polyA usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
RNA stability	BLA	Brain	Eye	IC	IL	LHb	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

BLA • Brain • Eye • IC • IL • LHb • 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.

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

Covariates used for xQTL mapping

Expression	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Isoform ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Intron excision ratio	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative TSS usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
Alternative polyA usage	BLA	Brain	Eye	IC	IL	LHb	NAcc	OFC	PL	pVTA	RMTg
RNA stability	BLA	Brain	Eye	IC	IL	LHb	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 for the IL, LHb, NAcc, OFC, and PL brain regions are available in SRA and can be accessed from GEO accession GSE173141.
RNA-Seq reads for Eye are available at GEO accession GSE201236.
RNA-Seq reads for Adipose are available at GEO accession GSE196572.
RNA-Seq reads for Liver are available at GEO accession GSE200453.

Original study data

Archives of the data files used in the originating studies.