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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.

Gene expression

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

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

TPM (transcripts per million) Relative abundance of transcripts

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

Inverse-quantile normalized Used for eQTL mapping

Adipose | BLA | 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.

eQTL covariates

Adipose | BLA | 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 | 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

Adipose | BLA | 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