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Series GSE47875 Query DataSets for GSE47875
Status Public on Aug 08, 2014
Title SEQC Toxicogenomics Study: microarray data set
Organism Rattus norvegicus
Experiment type Expression profiling by array
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.

contributor: DrugMatrix, National Toxicology program (NTP)
 
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.
 
Contributor(s) Auerbach SS, Tong W
Citation(s) 25150839, 30420870, 25977778, 33354967
Submission date Jun 12, 2013
Last update date Feb 22, 2021
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 (1)
GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
Samples (105)
GSM1161420 Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep1
GSM1161421 Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep2
GSM1161422 Rat_Liver_ECONAZOLE_334mg/kg_5d_NU_OG_Rep3
This SubSeries is part of SuperSeries:
GSE47792 SEQC Project
Relations
BioProject PRJNA208229

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
GSE47875_RAW.tar 263.2 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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