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Series GSE199986 Query DataSets for GSE199986
Status Public on Apr 01, 2022
Title Liver RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary As part of the PhenoGen Project (https://phenogen.org), liver RNA-Seq data has been collected from strains of the Hybrid Rat Diversity Panel (HRDP). RNA expression levels were estimated using high throughput RNA sequencing (RNA-Seq) on long (>200 nucleotides) RNAs, i.e., total RNA where ribosomal RNA was depleted. These data can be used to examine predisposition phenotypes in the HRDP. Processed data and interactive graphics are also available through the PhenoGen website. Additional data from additional strains will be added as they become available.
 
Overall design RNA expression data has been gathered over several tissues (e.g., brain, liver, heart, kidney) on rats from the Hybrid Rat Diversity Panel (HRDP) as part of the RGAP: The heritable transcriptome and alcoholism project funded by NIAAA R24 AA013162. For each strain, RNA from 3 naive male biological replicates is extracted and a separate RNA-Seq library is generated from each replicate. rRNA-depleted total RNA is used to generate libraries and libraries are sequenced using Illumina sequencing technology. All rats used in this study were alcohol and drug naive and were NOT subjected to any behavioral testing. Therefore, these data represent a predisposition database that can be used for integrative systems genetics studies.
This dataset includes data from liver.
 
Contributor(s) Tabakoff B, Hoffman P, Saba L
Citation(s) 36186443
NIH grant(s)
Grant ID Grant title Affiliation Name
R24 AA013162 The Heritable Transcriptome and Alcoholism UNIVERSITY OF COLORADO DENVER Boris Tabakoff
Submission date Apr 01, 2022
Last update date Dec 18, 2023
Contact name Laura Saba
E-mail(s) Laura.Saba@cuanschutz.edu
Organization name University of Colorado Anschutz Medical Campus
Department Skaggs School of Pharmacy and Pharmaceutical Sciences
Street address 12850 E. Montview Blvd
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (3)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
GPL22396 Illumina HiSeq 4000 (Rattus norvegicus)
GPL25947 Illumina NovaSeq 6000 (Rattus norvegicus)
Samples (201)
GSM6001763 rRNA Depleted total RNA from liver from untreated ACI rats (replicate 1, sequencing batch 8)
GSM6001764 rRNA Depleted total RNA from liver from untreated ACI rats (replicate 2, sequencing batch 8)
GSM6001765 rRNA Depleted total RNA from liver from untreated ACI rats (replicate 3, sequencing batch 10)
This SubSeries is part of SuperSeries:
GSE199987 RNA expression levels in the Hybrid Rat Diversity Panel for the PhenoGen website (https://phenogen.org)
Relations
BioProject PRJNA822426
SRA SRP367038

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.gene.ensembl96.strainMeans.txt.gz 3.7 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.gene.ensembl96.txt.gz 8.1 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.strainMeans.txt.gz 17.0 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.gene.reconstruction.txt.gz 31.2 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.reconstruction.gtf.gz 5.7 Mb (ftp)(http) GTF
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.transcript.ensembl96.strainMeans.txt.gz 6.2 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.transcript.ensembl96.txt.gz 14.3 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.strainMeans.txt.gz 22.2 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v5.totalRNA.Liver.transcript.reconstruction.txt.gz 50.9 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.gene.ensemblRR.strainMeans.txt.gz 6.4 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.gene.ensemblRR.txt.gz 21.9 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.gene.reconstruction.strainMeans.txt.gz 15.1 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.gene.reconstruction.txt.gz 51.7 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.reconstruction.gtf.gz 5.0 Mb (ftp)(http) GTF
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.transcript.ensemblRR.strainMeans.txt.gz 9.9 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.transcript.ensemblRR.txt.gz 34.1 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.transcript.reconstruction.strainMeans.txt.gz 32.4 Mb (ftp)(http) TXT
GSE199986_PhenoGen.HRDP.v6.totalRNA.Liver.transcript.reconstruction.txt.gz 98.1 Mb (ftp)(http) TXT
GSE199986_readme.txt 1.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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