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Download unmerged data

Some tissues have RNA-seq datasets from multiple studies that were merged for the v3 release. This page contains input files and results for those individual datasets run without merging.

Gene expression

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

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

TPM (transcripts per million) Relative abundance of transcripts

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

Inverse-quantile normalized

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

Filtered inverse-quantile normalized Used for eQTL mapping

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

Other info

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

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

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.

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

Covariates used for eQTL mapping

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

eQTLs

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

All significant cis-eQTL variant-gene pairs

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

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.

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

sQTLs

Splice phenotypes Relative usage of splice junctions within junction clusters

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

Covariates used for sQTL mapping

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

All significant cis-sQTL variant-phenotype pairs

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3

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.

NAcc1 • NAcc2 • NAcc3 • PL1 • PL2 • PL3