In-depth characterization of XXXX -promoting cell transcriptome by RNA sequencing and microarrays.

@entity1 @entity0 @entity5 @entity2842 @entity1299 @entity687 @entity479
Numerous studies have reported the existence of @entity5 ( @entity5 ) with self-renewal potential and a relevant role in drug resistance. However, pathways and modifications involved in the maintenance of such @entity5 subpopulations are still only partially understood. Sequencing-based approaches offer the opportunity for a detailed study of @entity5 including their transcriptome modulation. Using microarrays and RNA sequencing approaches, we compared the transcriptional profiles of parental MCF7 @entity0 cells with MCF7-derived @entity5 (i.e. MCFS). Data were explored using different bioinformatic approaches, and major findings were experimentally validated. The different analytical pipelines (Lifescope and Cufflinks based) yielded similar although not identical results. RNA sequencing data partially overlapped microarray results and displayed a higher dynamic range, although overall the two approaches concordantly predicted pathway modifications. Several biological functions were altered in @entity5 , ranging from production of inflammatory cytokines (i.e., @entity687 and @entity2842 ) to proliferation and response to @entity479 hormones. More than 300 non-coding RNAs were defined as differentially expressed, and 2,471 potential splicing events were identified. A consensus signature of genes up-regulated in @entity5 was derived and was found to be significantly associated with insensitivity to @entity1299 in a @entity0 @entity1 dataset. Overall, we obtained a detailed portrait of the transcriptome of a @entity0 @entity5 line, highlighted the role of non-coding RNAs and differential splicing, and identified a gene signature with a potential as a context-specific biomarker in @entity1 receiving endocrine treatment.
