Computational protocol: Ovarian and Breast Cancer Spheres Are Similar in Transcriptomic Features and Sensitive to Fenretinide

Similar protocols

Protocol publication

[…] Total RNA from A2780, MCF7, and SUM159 parental and sphere cells were amplified and labeled with biotin according to the standard Affymetrix protocol. The fragmented, biotinylated cDNA was then subjected to hybridization with the GeneChip Human Genome-U133 Plus 2.0 array (Affymetrix, Santa Clara, CA). DAVID Bioinformatics Resources analyses of biological themes were performed to explore the underlying themes of those statistically significant differentially expressed genes in terms of biological relevance, for example, functional relevance as revealed by Gene Ontology (GO) enrichment analysis [] and regulatory relevance as revealed by UCSC conserved transcription factor binding site (TFBS) enrichment analysis []. The Benjamini-Hochberg-derived step-up procedure of False Discovery Rate (FDR) was applied to account for multiple hypothesis testing, thus to assess the significance of the biological theme enrichments. The transcriptome profilings of A2780, MCF7, and SUM159 parental and sphere cells are available at GEO accession GSE43657. […]

Pipeline specifications

Software tools DAVID, CONFAC
Application ChIP-on-chip analysis
Diseases Neoplasms, Ovarian Neoplasms, Hereditary Breast and Ovarian Cancer Syndrome
Chemicals Cisplatin, Fenretinide