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Series GSE20465 Query DataSets for GSE20465
Status Public on Oct 22, 2010
Title Her2/Neu breast cancer mouse model whole tissue transcriptome
Organism Mus musculus
Experiment type Expression profiling by array
Summary Purpose: We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens.
Experimental design: Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias.
Results: In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate ≤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue.
Conclusions and clinical relevance: These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS. The availability of these datasets will contribute positively to clinical proteomics.
 
Overall design Affymetrix GeneChip Mouse Genome 430 2.0 microarrays were used to profile whole tissues from 5 different tissue types of 25 tumor-bearing and 25 control mice of the Her2/Neu breast cancer mouse model. The 5 tissues tested were from breast, liver, spleen, blood cell, and thymus. The tumor-bearing mice were bitransgenic for MMTV-rtTA/TetO-NeuNT, and the control mice were transgenic for TetO-NeuNT only. The control mice were age- and cage-matched to the tumor-bearing mice. All samples were lysed and total RNA isolated and amplified prior to hybridization.
 
Contributor(s) Schoenherr RM, Kelly-Spratt KS, Lin C, Whiteaker JR, Liu T, Holzman T, Coleman I, Feng L, Lorentzen TD, Krasnoselsky AL, Wang P, Liu Y, Gurley KE, Amon LM, Schepmoes AA, Moore RJ, Camp II DG, Chodosh LA, Smith RD, Nelson PS, McIntosh MW, Kemp CJ, Paulovich AG
Citation(s) 21448875
Submission date Feb 22, 2010
Last update date Feb 11, 2019
Contact name Regine M Schoenherr
Organization name Fred Hutchinson Cancer Research Center
Street address 1100 Fairview Ave N, LE-360
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (250)
GSM513371 breast_tumor_sample_TL20070522_5_A1
GSM513372 normal breast from control mouse_sample_TL20070522_5_A2
GSM513373 breast_tumor_sample_TL20070522_5_A3
Relations
BioProject PRJNA125129

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
GSE20465_RAW.tar 939.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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