Transcription profiling of 51 human breast cancer cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Parkinson Helen
PROVIDER: S-ECPF-MTAB-7 | biostudies-other |
REPOSITORIES: biostudies-other
Similar Datasets
Project description:We measured baseline gene expression profiles for a panel of 51 breast cancer cell lines using the Affymetrix U133A array.
| S-ECPF-TABM-157 | biostudies-other
Project description:Total RNA from 46 breast cell lines was labelled using the Illumina TotalPrep RNA Amplification kit (Ambion) following manufacturer's instructions. 1.5 µg of biotin-labelled cRNA were used for each hybridisation on Sentrix Human-6 v1 BeadChips (Illumina, San Diego, CA) following manufacturer's protocol.
| S-ECPF-TABM-827 | biostudies-other
Project description:Gene expression analysis on growing breast cancer cell lines. Experiment Overall Design: see Bild, A. et.al.
| S-ECPF-GEOD-3156 | biostudies-other
Project description:Transcriptional profiling was conducted on RNA from 23 breast cancer cell lines to identify genes whose expression level correlates with sensitivity of particular drug Experiment Overall Design: Baseline gene expression profiling was performed using 23 breast cancer cell lines to identify genomic signatures highly correlated with in vitro sensitivity to a particular drug
| S-ECPF-GEOD-6569 | biostudies-other
Project description:INTRODUCTION: Breast cancer is a genetically and phenotypically complex disease. To understand the role of miRNAs in this molecular complexity, we performed miRNA expression analysis in a cohort of molecularly well-characterized human breast cancer cell lines to identify miRNAs associated with the most common molecular subtypes and the most frequent genetic aberrations. METHODS: Using a microarray carrying LNA™ modified oligonucleotide capture probes), expression levels of 725 human miRNAs were measured in 51 breast cancer cell lines. Differential miRNA expression was explored by unsupervised cluster analysis and was then associated with the molecular subtypes and genetic aberrations commonly present in breast cancer. RESULTS: Unsupervised cluster analysis using the most variably expressed miRNAs divided the 51 breast cancer cell lines into a major and a minor cluster predominantly mirroring the luminal and basal intrinsic subdivision of breast cancer cell lines. One hundred and thirteen miRNAs were differentially expressed between these two main clusters. Forty miRNAs were differentially expressed between basal-like and normal-like/claudin-low cell lines. Within the luminal-group, 39 miRNAs were associated with ERBB2 overexpression and 24 with E-cadherin gene mutations, which are frequent in this subtype of breast cancer cell lines. In contrast, 31 miRNAs were associated with E-cadherin promoter hypermethylation, which, contrary to E-cadherin mutation, is exclusively observed in breast cancer cell lines that are not of luminal origin. Thirty miRNAs were associated with p16INK4 status while only a few miRNAs were associated with BRCA1, PIK3CA/PTEN and TP53 mutation status. Twelve miRNAs were associated with DNA copy number variation of the respective locus. CONCLUSION: Luminal-basal and epithelial-mesenchymal associated miRNAs determine the subdivision of miRNA transcriptome of breast cancer cell lines. Specific sets of miRNAs were associated with ERBB2 overexpression, p16INK4a or E-cadherin mutation or E-cadherin methylation status, which implies that these miRNAs may contribute to the driver role of these genetic aberrations. Additionally, miRNAs, which are located in a genomic region showing recurrent genetic aberrations, may themselves play a driver role in breast carcinogenesis or contribute to a driver gene in their vicinity. In short, our study provides detailed molecular miRNA portraits of breast cancer cell lines, which can be exploited for functional studies of clinically important miRNAs.
| S-EPMC3672661 | biostudies-literature
Project description:A cell line comparison experiment for breat cancer 51 cancer cell lines
2008-02-23 | E-MTAB-7 | biostudies-arrayexpress
Project description:We measured baseline gene expression profiles for a panel of 51 breast cancer cell lines using the Affymetrix U133A array.
2006-11-21 | E-TABM-157 | biostudies-arrayexpress
Project description:Basal gene expression levels were determined by global gene expression profiling of breast cancer cell lines. Molecular subtype was determined using gene expression and HER2 status assesses by HER2 FISH analysis. Experiment Overall Design: RNA was prepared from cell lines cultured in 10% fetal bovine serum
2009-01-17 | E-GEOD-12777 | biostudies-arrayexpress
Project description:Basal gene expression levels were determined by global gene expression profiling of breast cancer cell lines. Molecular subtype was determined using gene expression and HER2 status assesses by HER2 FISH analysis. Keywords: Basal gene expression (no stimulation or timecourse)
2009-01-12 | GSE12777 | GEO
Project description:Breast cancer subtypes identified in genomic studies have different underlying genetic defects. Mutations in the tumor suppressor p53 occur more frequently in estrogen receptor (ER) negative, basal-like and HER2-amplified tumors than in luminal, ER positive tumors. Thus, because p53 mutation status is tightly linked to other characteristics of prognostic importance, it is difficult to identify p53's independent prognostic effects. The relation between p53 status and subtype can be better studied by combining data from primary tumors with data from isogenic cell line pairs (with and without p53 function). In this study, the p53-dependent gene expression signatures of four cell lines (MCF-7, ZR-75-1, and two immortalized human mammary epithelial cell lines) were identified by comparing p53-RNAi transduced cell lines to their parent cell lines. Cell lines were treated with vehicle only or doxorubicin to identify p53 responses in both non-induced and induced states. Each cell line displayed unique patterns of gene expression, but cell type specific trends were evident. A common gene expression signature associated with p53 loss across all four cell lines was identified. This signature showed overlap with the signature of p53 loss in primary breast tumors and predicted relapse-free survival and overall survival in independent test data sets. Experiment Overall Design: We analyzed 48 arrays performed using 48 polyA RNA samples. RNAs were collected from cell lines treated with an IC50 dose of doxorubicin hydrochloride or with a feeding control. Each cell line had its own reference which represented the second sample on the dual channel array. These untreated RNAs were prepared by pooling four harvests of that cell line at 60-80% confluence and 48h after feeding
| S-ECPF-GEOD-3178 | biostudies-other