Breast cancer data set (JFCR)

Title:: Gene expression profiling of LCM captured breast cancer cells
Summary:: The purpose of this study is to obtain comprehensive gene expression plofiles in breast cancer. Mammary gland cells were specifically isolated from 508 clinical tissue samples by laser capture microdissection (LCM). Total RNAs were extracted from LCM captured samples. We investigated gene expression profiles in 492 patients with breast cancer and 16 non-tumor tissues as a normal control using an Affymetrix GeneChip.
Overall design:: Mammary gland cells were captured from clinical tissues of breast cancer patient by LCM. Gene expression profilings for 492 tumor and 16 non-tumor samples were acquired using GeneChip Human Genome U133 Plus 2.0 (Affymetrix, Santa Clara, CA). Microarray datasets were normalized and transformed to log2 values using robust multi-array average (RMA) method with R statistical software and BioConductor package.

Treatment protocol	Mammary grand cells were isolated from frozen tissue sections using laser capture microdissection.
Extract protocol	Total RNA was extracted by Qiagen RNeasy kit according to the manufacturer's instructions.
Label protocol	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hyb protocol	Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
Scan protocol	GeneChips were scanned using the Affymetrix Genechip Scanner 3000.
Data processing	Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.
Value definition	RMA signal intensity

RMA normalized data (zipped, tab-separated text format, 213MB): Breast508-rma.zip