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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.

RNA-Seq DNA-Seq Microarray Genomic Marker Publications
Data Files for "Insight into genetic regulation of miRNA in mouse brain" by Kordas, G. et. al. (submitted, BMC Genomics)
Data Files
Small RNA-Seq on Geo

Data Files for "Condition-adaptive fusion graphical lasso (CFGL): an adaptive procedure for inferring condition-specific gene co-expression network." by Lyu, Y., Xue, L., Zhang, F., Koch, H., Saba, L., Kechris, K., & Li, Q. (in press, PLoS Computational Biology)
Data Files
Normalized Expression/Raw CEL Files

Data Files for "Predictive Modeling of miRNA-mediated Predisposition to Alcohol-related Phenotypes in Mouse" by Pratyaydipta Rudra et al. (submitted, BMC Genomics)
Data Files
Fastq Files
Processed Data

Data Files for "miR-MaGiC improves quantification accuracy for small RNA-seq." by Pamela Russell et al. (2018 May 15, BMC Res Notes)Abstract
Data Files
Fastq Files

Data Files for "Systems Genetic Analysis of Brown Adipose Tissue Function" by Michal Pravenec, Laura Saba, Vaclav Zidek, Vladimir Landa, Petr Mlejnek, Jan Silhavy, Miroslava Simakova, Hynak Strnad, Jaroslava Trnovska, Vojtech Skop, Martina Huttl, Irena Markova, Olena Oliyarnyk, Hana Malinska, Ludmila Kazdova, Harry Smith, and Boris Tabakoff. (Nov 10, 2017, Physiol Genomics.)Abstract
Data Files
CEL Files
Normalized Gene Array
WGCNA Module Data

Data Files used in "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

Data Files used in "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

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