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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 • IL • LHb • Liver • NAcc • OFC • PL • pVTA • RMTg

TPM (transcripts per million) Relative abundance of transcripts

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

Inverse-quantile normalized

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

Filtered inverse-quantile normalized Used for eQTL mapping

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

Genotypes

In this version, rats in the Adipose and Liver cohort are in the `round10_4` genotypes, and all others are in the `round10_5` genotypes. The included variants may differ between the two genotype files.

• ratgtex_v3_round10_4.rn7.vcf.gz
• ratgtex_v3_round10_5.rn7.vcf.gz

Other info

Rat info (all tissues)

Sample info (all tissues)

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

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

Covariates used for eQTL mapping

Adipose • BLA • Brain • Eye • IL • LHb • Liver • 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

Adipose • BLA • Brain • Eye • IL • LHb • Liver • 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.

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

sQTLs

Splice phenotypes Relative usage of splice junctions within junction clusters

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

Covariates used for sQTL mapping

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

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

All significant cis-sQTL variant-phenotype pairs

Adipose • BLA • Brain • Eye • IL • LHb • Liver • 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 sQTLs.

trans-sQTLs
All SNP-phenotype 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 • 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 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.