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GenomicsGenome-wide maps of H3K4me2 and DNase I hypersensitivity sites in prostate cancer cell line LNCaP and breast cancer cell line MCF-7.
We report the high-throughput profiling of histone modification and DNase I hypersensitivity sites in prostate cancer and breaset cancer cells. We found that while AR binding is associated with nucleosome depletion, ER binding is not. We showed that a quantitative measure of DNase I hypersensitivity...
ORGANISM(S): Homo sapiens 
2012-03-25 | E-GEOD-33216 | biostudies-arrayexpress
GenomicsGenome-wide maps of H3K4me2/3 in prostate cancer cell line LNCaP
We report the high-throughput profiling of histone modifications in prostate cancer cells. By obtaining over 1 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of prostate cancer cells. we found androgen treatment dismisses a nucleosome o...
ORGANISM(S): Homo sapiens 
2010-03-09 | E-GEOD-20042 | 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
TranscriptomicsAltered antisense-to-sense transcript ratios in breast cancer: Agilent
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-26000 | biostudies-arrayexpress
TranscriptomicsAltered antisense-to-sense transcript ratios in breast cancer: ASSAGE
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-25932 | biostudies-arrayexpress
GenomicsmodENCODE_Lieb and White Lab: unltra-deep sequencing data of genomic DNA, chromatin input, and ChIP of Su(Hw) and H3K36me3 from S2 cells on Illumina Genome Analyzer.
This is a dataset generated by the modENCODE Project. It contains both the pair-end and single-end sequencing data of genomic DNA, chromatin input and the ChIP of the factors Su(Hw) and H3K36me3 from Drosophila S2 cells and it was generated on Illumina Genome Analyzer. The goal was to sequence ~120M...
ORGANISM(S): Drosophila melanogaster 
2011-03-04 | E-GEOD-27679 | 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
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