Project description:We looked for difference in genetic expression in 4 cell lines that have the same genetic background but reproduce breast cancer progression. Especially, we identied genes that were overexpressed in late cancer progression (MCFT1 and MCFCA1) but not in early stages (MCF10A and MCFNeoT).
Project description:Microarrays were used to detail the global programme of gene expression underlying breast cancer cell lines. We identified two main groups of luminal-type and basal-type breast cancer cell lines by unsupervised Pearson correlation of breast cancer cell lines and intrinsic subtyping. Supervised analysis on spindle versus non-spindle breast cancer cell lines identified a spindle cell signature of 1,144 genes identifying all spindle, basal-type, E-cadherin methylated breast cancer cell lines.
Project description:Triplicate analysis of eleven breast cancer cell lines, each separated to 12 offgel fractions. Proteomes were quantified relative to heavy SILAC-labeled MCF7 cells that served as a spike-in standard. In this study, we used system-wide analysis of breast cancer proteomes to identify proteins that are associated with the progression of ER(-) tumors. Our two-step approach included an initial deep analysis of cultured cells that were obtained from tumors of defined breast cancer stages, followed by a validation set using human breast tumors. Using high-resolution mass spectrometry and quantification by Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC), we identified 8,750 proteins and quantified 7,800 of them. A stage-specific signature was extracted and validated by mass spectrometry and immunohistochemistry on tissue microarrays. Data analysis: Raw MS files from the LTQ-Orbitrap were analyzed by MaxQuant (version 1.1.1.9). MS/MS spectra were searched against the decoy IPI-human database version 3.68 containing both forward and reverse protein sequences by the Andromeda search engine. For identification, the false discovery rate (FDR) was set to 0.01 on the protein and on the peptide levels.
Project description:This SuperSeries is composed of the following subset Series: GSE31603: Human breast cancer cell lines: vehicle vs. BMP4 incubation GSE31604: Human breast cancer cell lines: vehicle vs. BMP7 incubation Refer to individual Series
Project description:miRNA expression is often disregulated in cancer pathways, such as progression of resistance. We used microarrays in order to determine the differences in miRNA expression between breast cancer cell lines and their resistant pairs.
Project description:Microarrays were used to detail the global programme of gene expression underlying breast cancer cell lines. We identified two main groups of luminal-type and basal-type breast cancer cell lines by unsupervised Pearson correlation of breast cancer cell lines and intrinsic subtyping. Supervised analysis on spindle versus non-spindle breast cancer cell lines identified a spindle cell signature of 1,144 genes identifying all spindle, basal-type, E-cadherin methylated breast cancer cell lines. Breast cancer cell lines were grown to optimal cell densities for RNA extraction and hybridization on Affymetrix microarrays.