PhenoGen Informatics
The site for quantitative genetics of the transcriptome.
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Select the download icon() to download data from any of the datasets below. For some data types multiple options may be available. For these types, a window displays that allows you to choose specific files.

UCSC Track Hubs REST API / R RNA-Seq DNA-Seq Microarray Genomic Marker Publications
A Genetically Based Gene Expression Network for Responding to Salt by Hypertensive and Normotensive Animals.
(C. Wood et. al. - submitted)
Data Files
Gene Expression Values
SBP Phenotype
SNPs Mapping
MD5 Checksums


Evaluation and characterization of expression quantitative trait analysis methods in the Hybrid Rat Diversity Panel
(J. Pattee et. al., 2022 - Front Genet.)
Abstract
Data Files
Raw Genotype Data
SNP Meta Data
Kinship Matrix
Read Me
MD5 Checksums


Beyond genes: Inclusion of alternative splicing and alternative polyadenylation to assess the genetic architecture of predisposition to voluntary alcohol consumption in brain of the HXB/BXH recombinant inbred rat panel
( R. Lusk et. al., 2022, Front. Genet.)
Abstract
Data Files
Alcohol Consumption
SNPs for Mapping
Processed Expression Data
Final DABG transcriptome GTF
Strain Specific Genomes
MD5 Checksum


A Long Non-Coding RNA (Lrap) Modulates Brain Gene Expression and Levels of Alcohol Consumption in Rats
( L. Saba et. al., 2021, Genes, Brain and Behavior)
Abstract
Data Files
WT/KO Transcriptome GTF
Gene/Isoform Count Matrices


Insight into genetic regulation of miRNA in mouse brain.
(G. Kordas et. al., 2019, BMC Genomics)
Abstract
Population Data Files
ILS/ISS(LXS) miRNA eQTLs
Small RNA-Seq on GEO


Condition-adaptive fusion graphical lasso (CFGL): an adaptive procedure for inferring condition-specific gene co-expression network.
(Y. Lyu et al., 2018, PLoS Computational Biology)
Abstract
Data Files
Normalized Expression/Raw CEL Files


Predictive Modeling of miRNA-mediated Predisposition to Alcohol-related Phenotypes in Mouse.
(Pratyaydipta Rudra et al., 2018, BMC Genomics)
Abstract
Data Files
Fastq Files
Processed Data
Markers


miR-MaGiC improves quantification accuracy for small RNA-seq
(Pamela Russell et al., 2018, BMC Res Notes)
Abstract
Data Files
Fastq Files


Systems Genetic Analysis of Brown Adipose Tissue Function.
(Michal Pravenec et al. 2017, Physiol Genomics.)
Abstract
Data Files
CEL Files
Normalized Gene Array
WGCNA Module Data


Uncovering the liver's role in immunity through RNA co-expression networks.
(Harrall et. al. 2016, Mamm. Genome)
Abstract
Data Files
Array Masks
Cell Type Specific Normalized Exon Array
HXB Normalized Exon Array
Reconstructed Liver Transcriptome
RNA-Seq
SDPs


The sequenced rat brain transcriptome, its use in identifying networks predisposing alcohol consumption
(Saba et. al. 2015, FEBS)
Abstract
Population Data Files
BN-Lx/SHR Reconstructed Brain Transcriptome
HXB/BXH SNPs used for alcohol consumption QTL
HXB/BXH Alcohol Consumption (2 bottle choice, 10% ethanol, week 2)
HXB/BXH Normalized exon array data - gene level
HXB/BXH Normalized exon array data - isoform level
Selected Lines Normalized exon array data - gene level
Selected Lines Normalized exon array data - isoform level
N/A Array Masks


Whole Brain and Brain Regional Coexpression Network Interactions Associated with Predisposition to Alcohol Consumption
(Vanderlinden et. al., 2013, PLOS)
Abstract
Population Data Files
BXD BXD Whole Brain Expression Data for WGCNA
BXD Module Membership Key
BXD Module Eigengene Matrix