PhenoGen - Download Resources

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

Expression Data Files

Experiment Accession ID	Organism	Dataset	Tissue	Array	Masks
257	Mouse	Public BXD RI Mice	Whole Brain	Affymetrix GeneChip Mouse Genome 430 2.0 [Mouse430_2]
707	Mouse	Public ILSXISS RI Mice	Whole Brain	Affymetrix GeneChip Mouse Exon 1.0 ST Array
258	Mouse	Public Inbred Mice	Whole Brain	Affymetrix GeneChip Mouse Genome 430 2.0 [Mouse430_2]
261	Rat	Public HXB/BXH RI Rats	Whole Brain	GE Healthcare CodeLink Rat Whole Genome Bioarray
730	Rat	Public HXB/BXH RI Rats (Brain, Exon Arrays)	Whole Brain	Affymetrix GeneChip Rat Exon 1.0 ST Array	*
729	Rat	Public HXB/BXH RI Rats (Heart, Exon Arrays)	Heart	Affymetrix GeneChip Rat Exon 1.0 ST Array	*
727	Rat	Public HXB/BXH RI Rats (Liver, Exon Arrays)	Liver	Affymetrix GeneChip Rat Exon 1.0 ST Array	*
760	Rat	Public HXB/BXH RI Rats (Brown Adipose, Exon Arrays)	Brown Adipose	Affymetrix GeneChip Rat Exon 1.0 ST Array	*

*The mask files are the same for all of these datasets.

Organism	Panel	Source
Mouse	BXD	Wellcome-CTC Mouse Strain SNP Genotype Set
Mouse	LXS	Affymetrix Mouse Diversity SNP Array
Rat	HXB/BXH	STAR consortium

New RNA Sequencing Datasets Experimental Details/Downloads

Description	Organism	Strain	Tissue	Seq. Tech.	RNA Type	Read Type	Genome Versions	Experimental Details	Raw Data Downloads	Result Downloads
Whole Brain from ILS/ISS Parental Strains	Mm	ILS/ISS	Whole Brain	Illumina HiSeq 2000	smallRNA	51bp single-end reads	mm10

RNA Sequencing BED/BAM Data Files

Organism	Strain	Tissue	Seq. Tech.	RNA Type	Read Type	Genome Versions
Rat	BN-Lx/CubPrin	Brain	Illumina HiSeq2000	polyA+ (>200 nt) selected	100 bp paired-end	Rn6, Rn5
Rat	SHR/OlaIpcvPrin	Brain	Illumina HiSeq2000	polyA+ (>200 nt) selected	100 bp paired-end	Rn6, Rn5
Rat	BN-Lx/CubPrin	Brain	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	100 bp paired-end	Rn6, Rn5
Rat	SHR/OlaIpcvPrin	Brain	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	100 bp paired-end	Rn6, Rn5
Rat	BN-Lx/CubPrin	Brain	Illumina HiSeq2000	small RNA (<200 nt) selected	50 bp single-end	Rn5
Rat	SHR/OlaIpcvPrin	Brain	Illumina HiSeq2000	small RNA (<200 nt) selected	50 bp single-end	Rn5
Rat	BN-Lx/CubPrin	Brain	Helicos	total RNA (>200 nt) after ribosomal RNA depletion	~33 bp single-end	Rn5
Rat	SHR/OlaIpcvPrin	Brain	Helicos	total RNA (>200 nt) after ribosomal RNA depletion	~33 bp single-end	Rn5
Rat	BN-Lx/CubPrin	Heart	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	stranded 100 bp paired-end	Rn6
Rat	SHR/OlaIpcvPrin	Heart	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	stranded 100 bp paired-end	Rn6
Rat	BN-Lx/CubPrin	Liver	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	stranded 100 bp paired-end	Rn6
Rat	SHR/OlaIpcvPrin	Liver	Illumina HiSeq2000	total RNA (>200 nt) after ribosomal RNA depletion	stranded 100 bp paired-end	Rn6

RNA-Seq Transcriptome Reconstruction

Organism	Strains	Tissue	Assembled by
Rat	BN-Lx/CubPrin,SHR/OlaIpcvPrin	Whole Brain	Cufflinks
Rat	BN-Lx/CubPrin,SHR/OlaIpcvPrin	Heart	Cufflinks
Rat	BN-Lx/CubPrin,SHR/OlaIpcvPrin	Liver	Cufflinks
Rat	BN-Lx/CubPrin,SHR/OlaIpcvPrin	Whole Brain	Cufflinks

Organism	Strain	Seq. Tech.	Genome Version
Rat	BN-Lx/CubPrin	Illumina HiSeq2000	Rn6, Rn5
Rat	SHR/OlaIpcvPrin	Illumina HiSeq2000	Rn6, Rn5
Rat	SHR/NCrlPrin	Illumina HiSeq2000	Rn5
Rat	presumptive F344*	Illumina HiSeq2000	Rn5

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
Markers

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
RNA-Seq
SDPs

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

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.

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