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See the About page for processing and data format specifications.

Gene info

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.

Gene expression

Median TPM per gene per tissue Used for heatmap visualizations

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

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

TPM (transcripts per million) Relative abundance of transcripts

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

Inverse-quantile normalized Used for eQTL mapping

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

Genotypes

Genotypes are grouped by the datasets from which they originated. The sample sets for the tissues within a dataset are overlapping subsets. Different datasets include different sets of SNPs in their genotypes.

Other info

Rat IDs The final QC-filtered sample sets used for eQTL mapping
The NAcc2 dataset contains some samples with single-end (SE) RNA-Seq reads and other samples with paired-end (PE) reads.

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 (SE)(PE) | OFC | PL | PL2

RNA-Seq FASTQ file lists with corresponding rat IDs
Datasets with single-end reads have one column of files, while paired-end file pairs are given as two columns. These lists may include files for samples that were filtered out, so use the rat ID lists above to get the final sample sets.
The NAcc2 dataset contains some samples with single-end (SE) RNA-Seq reads and other samples with paired-end (PE) reads.

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 (SE)(PE) | OFC | PL | PL2

Covariates used for eQTL mapping

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

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 | NAcc2 | OFC | PL | PL2

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 | NAcc2 | OFC | PL | PL2

sQTLs

Splice phenotypes Relative usage of splice junctions within junction clusters

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

Covariates used for sQTL mapping

Adipose | BLA | Brain | Eye | IL | LHb | Liver | NAcc | NAcc2 | OFC | PL | PL2

Conditionally independent cis-sQTLs
A table of cis-sQTLs 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 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 | NAcc2 | OFC | PL | PL2

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.

Original study data

The processed data above may differ from the results reported in each original study for a couple reasons:

  1. Different processing decisions could be made for each study, while the data in this portal are processed uniformly to facilitate comparison across tissues.
  2. The published study results are immutable, while new versions of data in this portal may be released, for example to improve quality or to use updated reference genome and annotations.
Therefore, we also provide data files here corresponding directly to the results in each paper.

IL, LHb, NAcc, OFC, PL

The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats

Eye

Manuscript under review