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Series GSE55347 Query DataSets for GSE55347
Status Public on Aug 08, 2014
Title SEQC Toxicogenomics Study: RNA-Seq data set
Organism Rattus norvegicus
Experiment type Expression profiling by high throughput sequencing
Summary The comparative advantages of RNA-Seq and microarrays in transcriptome profiling were evaluated in the context of a comprehensive study design. Gene expression data from Illumina RNA-Seq and Affymetrix microarrays were obtained from livers of rats exposed to 27 agents that comprised of seven modes of action (MOAs); they were split into training and test sets and verified with real time PCR.
 
Overall design 105 samples were selected from the DrugMatirx tissue/RNA bank that is now owned by the National Toxicology Program (NTP). The samples were split into 2 sets, training and test, to allow for the evaluation of classifiers derived from the data. There were 63 samples in the training set and 42 in the test set. Of the 63 samples in the training set 45 were derived from rats treated with test agent and 18 were control samples (3 sets of 6). 39 of the test set samples were derived from test agent treated animals and 6 were from vehicle and route matched controls. Five MOAs were represented in the training set and 4 MOAs were in the test set. Two of the MOAs were duplicated from the test set and two were without representation in the training set. For each test agent there were three rats treated, in accordance with the common practice in the field of toxicology. For each MOA there were three representative test agents to ensure adequate power for detecting the MOA signatures. 6 samples from the training set had duplicate libraries sequenced and duplicate sequencing runs for the first library.
DrugMatrix, National Toxicology program (NTP)
Sequencing was carried out in Dr. Charles Wang's Functional Genomics Core at City of Hope Comprehensive Cancer Center, Duarte, CA
 
Contributor(s) Wang C, Auerbach SS, Shi L, Tong W
Citation(s) 25150839, 30420870, 25977778
Submission date Feb 25, 2014
Last update date Jun 17, 2019
Contact name Leming Shi
E-mail(s) lemingshi@fudan.edu.cn
Phone +86-18616827008
Organization name Fudan University
Department School of Life Sciences
Lab Center for Pharmacogenomics
Street address 2005 Songhu Road
City Shanghai
ZIP/Postal code 200438
Country China
 
Platforms (2)
GPL14844 Illumina HiSeq 2000 (Rattus norvegicus)
GPL17116 Illumina HiScanSQ (Rattus norvegicus)
Samples (116)
GSM1336184 In Vivo Rat Liver Carcinogen (COH_WANG_AB0142ACXX_97922_L_PHE_NN_OG_ACAGTG_s_1)
GSM1336185 In Vivo Rat Liver Carcinogen (COH_WANG_AB0142ACXX_97998_L_PHE_NN_OG_ACAGTG_s_2)
GSM1336186 In Vivo Rat Liver Carcinogen (COH_WANG_AB0142ACXX_98379_L_PIR_NN_OG_GCCAAT_s_4)
This SubSeries is part of SuperSeries:
GSE47792 SEQC Project
Relations
BioProject PRJNA239561
SRA SRP039021

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Supplementary file Size Download File type/resource
GSE55347_Magic_Pipeline.pdf.gz 94.4 Kb (ftp)(http) PDF
GSE55347_TGxSEQC_GeneExpressionIndex_Magic_20120831_116samples.txt.gz 6.6 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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