Transcriptomics

Dataset Information

67

All Tumor Sector Experiments (T1-T20)


ABSTRACT: This SuperSeries is composed of the following subset Series: GSE16598: Tumor T1 Sectors GSE16599: Tumor T2 Sectors GSE16600: Tumor T3 Sectors GSE16601: Tumor T4 Sectors GSE16602: Tumor T5 Sectors GSE16603: Tumor T6 Sectors GSE16604: Tumor T7 Sectors GSE16605: Tumor T8 Sectors GSE16606: Tumor T9 Sectors GSE16607: Tumor T10 Sectors GSE16608: Tumor T11 Sectors GSE16609: Tumor T12 Sectors GSE16610: Tumor T13 Sectors GSE16611: Tumor T14 Sectors GSE16663: Tumor T15 Sectors GSE16664: Tumor T16 Sectors GSE16665: Tumor T17 Sectors GSE16667: Tumor T18 Sectors GSE16668: Tumor T19 Sectors GSE16669: Tumor T20 Sectors ROMA CGH experiments were conducted on four to six dissected sectors (S1-S6) from single primary ductal carcinomas (T1-T20). T1-T4 were analyzed by sectoring and analysis by ROMA. T5-T20 were analyzed using the Sector-Ploidy-Profiling (SPP) Approach. SPP involves macro-dissecting the tumor, flow-sorting nuclei by differences in total genomic DNA content and profiling the genome of the tumor subpopulations. The genomic DNA from each tumor was labeled with Cy5 and a reference fibroblast genome was labeled with Cy3 and cohybridized to a ROMA microarray (85K or 390K). Experiments were performed in color-reversal by dye-swapping samples and hybridizing the labeled DNA to a second microarray for T1-T15 experiments, but not for T16-T20 experiments.

ORGANISM(S): Homo sapiens  

SUBMITTER: Nicholas Navin 

PROVIDER: E-GEOD-16672 | ArrayExpress | 2009-07-10

SECONDARY ACCESSION(S): GSE16672PRJNA117387

REPOSITORIES: GEO, ArrayExpress

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Publications

High-resolution nucleosome mapping reveals transcription-dependent promoter packaging.

Weiner Assaf A   Hughes Amanda A   Yassour Moran M   Rando Oliver J OJ   Friedman Nir N  

Genome research 20091021 1


Genome-wide mapping of nucleosomes has revealed a great deal about the relationships between chromatin structure and control of gene expression, and has led to mechanistic hypotheses regarding the rules by which chromatin structure is established. High-throughput sequencing has recently become the technology of choice for chromatin mapping studies, yet analysis of these experiments is still in its infancy. Here, we introduce a pipeline for analyzing deep sequencing maps of chromatin structure an  ...[more]

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