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TranscriptomicsHMGA1: A master regulator of tumor progression in triple-negative breast cancer cells
Emerging evidence suggests that tumor cells metastasize by co-opting stem cell transcriptional networks, although the molecular underpinnings of this process are poorly understood. Here, we show for the first time that the high mobility group A1 (HMGA1) gene drives metastatic progression in triple ...
ORGANISM(S): Homo sapiens 
2015-02-18 | E-GEOD-45483 | biostudies-arrayexpress
TranscriptomicsGene expression profiling of human tissue samples using SAGE-Seq
We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes...
ORGANISM(S): Homo sapiens 
2010-10-05 | E-GEOD-24491 | biostudies-arrayexpress
GenomicsEpigenetic regulation of cell type-specific expression patterns in the human mammary epithelium [ChIP-Seq]
Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, and gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylati...
ORGANISM(S): Homo sapiens 
2011-03-01 | E-GEOD-26137 | biostudies-arrayexpress
TranscriptomicsAltered antisense-to-sense transcript ratios in breast cancer: Sage-Seq
Transcriptome profiling studies suggest that a large fraction of the genome is transcribed and many transcripts function independent of their protein coding potential. The relevance of noncoding RNAs (ncRNAs) in normal physiological processes and in tumorigenesis is increasingly recognized. Here, we...
ORGANISM(S): Homo sapiens 
2010-12-10 | E-GEOD-25291 | biostudies-arrayexpress
GenomicsEpigenetic regulation of cell type-specific expression patterns in the human mammary epithelium [MSDK-Seq]
Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, and gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylati...
ORGANISM(S): Homo sapiens 
2011-03-01 | E-GEOD-26139 | biostudies-arrayexpress
TranscriptomicsCombination of epigenetic, differentiation and DNA damaging agents induce tumor cell death and stem cell depletion in breast cancer
Gene expression profiles were performed on MDA-MB-231 TNBC cell line treated with entinostast, all-trans retinoic acid (ATRA), and doxorubicin as single, double, and triple combinations using Illumina. Treatment signatures were made from each drug treatment and integrated to find a comprehensive vie...
ORGANISM(S): Homo sapiens 
2014-11-18 | E-GEOD-63351 | biostudies-arrayexpress
TranscriptomicsDetection of hypermethylated circulating serum DNA in metastatic breast cancer and confirmation by the cMethDNA assay
The ability to consistently detect cell-free tumor-specific DNA in peripheral blood of patients with metastatic breast cancer provides the opportunity to detect changes in tumor burden and to monitor response to treatment. We developed cMethDNA, a quantitative multiplexed methylation specific PCR as...
ORGANISM(S): Homo sapiens 
2014-03-01 | E-GEOD-52621 | biostudies-arrayexpress
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