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Series GSE10797 Query DataSets for GSE10797
Status Public on Apr 03, 2008
Title Transcriptomes of breast epithelium and stroma in normal reduction mammoplasty and invasive breast cancer patients.
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The molecular basis of breast cancer invasion and metastasis is not well understood. Our objective was to analyze transcriptome differences between stromal and epithelial cells in normal breast tissue and invasive breast cancer to define the role stroma plays in invasion. Total RNA was isolated from epithelial and stromal cells that were laser captured from normal breast tissue (n=5) and invasive breast cancer (n=28). Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Differential gene expression was evaluated and compared within a model that accounted for cell type (epithelial [E] versus stromal [S]), diagnosis (cancer [C] versus normal [N]) as well as cell type-diagnosis interactions. Compared to NE, the CE transcriptome was highly enriched with genes in proliferative, motility and ECM ontologies. Differences in CS and NS transcriptomes suggested that the ECM was being remodeled in invasive breast cancer, as genes were over-represented in ECM and proteolysis ontologies. Genes more highly expressed in CS compared to CE were primarily ECM components or were involved in the remodeling of ECM, suggesting that ECM biosynthesis and remodeling were initiated in the tumor stromal compartment.
Keywords: cell type comparison, disease state analysis
Overall design Breast tissue was collected at surgery from patients undergoing surgical resection for invasive breast cancer (n=28) and reduction mammoplasty (n=5). Tissue was cryopreserved in OCT and serial sections were cut using a cryostat. Sections were stained and epithelial and stromal cells were isolated by laser capture microdissection. Total RNA was isolated and target was prepared using NuGen Ribo-SPIA Ovation Technology. Gene expression was measured using Affymetrix U133A 2.0 GeneChips. Gene expression differences were evaluated using a linear model of the Robust Multichip Average gene expression statistic, a model that accounted for cell type (E and S), patient diagnosis (C and N), as well as cell type-diagnosis interactions. Data were examined to determine false discovery rate and were filtered for fold changes in gene expression and p-value.
Contributor(s) Casey T, Bond J, Tighe S, Hunter T, Lintault L, Patel O, Eneman J, Crocker A, White J, Tessitore J, Stanley M, Harlow S, Weaver D, Muss H, Plaut K
Citation(s) 18373191
Submission date Mar 12, 2008
Last update date Dec 06, 2018
Contact name Jeffrey P Bond
Organization name University of Vermont
Department Microbiology and Molecular Genetics
Street address 95 Carrigan Dri e
City Burlington
State/province VT
ZIP/Postal code 05405
Country USA
Platforms (1)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
Samples (66)
GSM272671 cancer_epithelial_rep1
GSM272672 cancer_stroma_rep1
GSM272673 cancer_epithelial_rep2
BioProject PRJNA107497

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Supplementary file Size Download File type/resource
GSE10797_RAW.tar 104.8 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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