Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 6
Release date: Nov 1 2008
Last update date: Aug 10 2018
Access: Public
Diseases: Breast Neoplasms, Carcinoma, Ductal, Breast, Carcinoma, Lobular, Inflammatory Breast Neoplasms
Chemicals: Estrogens
Dataset link ERRγ mediates Tamoxifen resistance in novel models of invasive lobular breast cancer

Experimental Protocol


Total RNA was extracted from sub-confluent T-25 cm^2 tissue culture flasks of SUM44 and LCCTam cells, then processed and arrayed. Microarray data quality was then assessed using several tools, including those recommended by Affymetrix and a series of additional QC measures. The Robust Multiple-Array Average (RMA) method was used to preprocess the raw gene expression data, as implemented in the Bioconductor project (http://bioconductor.org). We then isolated a reduced dimension dataset that included genes that exhibit ≥2 fold change, p<0.05 and genes with intensity ≥log2(10) in both SUM44 and SUM44/LCCTam groups. Data visualization before and after dimensionality reduction was facilitated by multidimensional scaling as estimated using Principal Component Analysis (PCA) and Discriminant Component Analysis (DCA), to ensure that the global structure of the data was not altered by dimensionality reduction procedures.

Repositories


GEO

GSE12708

ArrayExpress

E-GEOD-12708

BioProject

PRJNA112729

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Contact


Rebecca Riggins
Rebecca B. Riggins