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Tumor T17 Sectors

ABSTRACT: The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T17) 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 subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were cohybridize to the same single microarray.

ORGANISM(S): Homo sapiens

SUBMITTER: Nicholas Navin

PROVIDER: E-GEOD-16665 | biostudies-arrayexpress |

REPOSITORIES: biostudies-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]

PMID: 19846608

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Tumor T16 Sectors

Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T16) 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 subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were cohybridize to the same single microarray.

2010-05-16 | E-GEOD-16664 | biostudies-arrayexpress

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients

Project description:Distinct molecular subtypes of breast carcinomas have been identified, but translation into clinical use has been limited. We have developed two platform independent algorithms to explore genomic architectural distortion using array comparative genomic hybridization (aCGH) data to measure 1) whole arm gains and losses (WAAI) and 2) complex rearrangements (CAAI). By applying CAAI and WAAI to data from 595 breast cancer patients we were able to separate the cases into eight subgroups with different distribution of genomic distortion. Within each subgroup data from expression analyses, sequencing and ploidy indicated that progression occurs along separate paths into more complex genotypes. Histological grade had prognostic impact only in the Luminal related groups while the complexity identified by CAAI had an overall independent prognostic power. This study emphasizes the relationship between structural genomic alterations, molecular subtype and clinical behavior, and provides a score of genomic complexity as a new tool for prognostication in breast cancer. Array CGH of 255 breast tumor samples vs a male skin fibroblast reference sample, in color reversal.

2009-12-15 | E-GEOD-19425 | biostudies-arrayexpress

Tumor T4 Sectors

Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T4). The genomic DNA from each tumor sector was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were dye-swapped and the experiments were conducted in color-reversal. The value data repesents a log ratio of the mean of two dye-swapped samples

2010-05-16 | E-GEOD-16601 | biostudies-arrayexpress

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Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T3). The genomic DNA from each tumor sector was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were dye-swapped and the experiments were conducted in color-reversal. The value data repesents a log ratio of the mean of two dye-swapped samples

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Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T6) 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 subpopulation was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were dye-swapped and the experiments were conducted in color-reversal. The value data repesents a log ratio of the mean of two dye-swapped samples

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Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T4) 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 subpopulation was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were dye-swapped and the experiments were conducted in color-reversal. The value data repesents a log ratio of the mean of two dye-swapped samples

2010-05-16 | E-GEOD-16602 | biostudies-arrayexpress

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2010-05-16 | E-GEOD-16669 | biostudies-arrayexpress

Tumor T19 Sectors

Project description:The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T19) 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 subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were cohybridize to the same single microarray.

2010-05-16 | E-GEOD-16668 | biostudies-arrayexpress

Tumor T18 Sectors

Project description:The following CGH experiments were conducted on four sectors (S1-S4) from a single primary ductal carcinoma tumor (T18) 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 subpopulation was labeled with Cy5 and hybridized to an 390K Rubble-Rep ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were cohybridize to the same single microarray.

2010-05-16 | E-GEOD-16667 | biostudies-arrayexpress

Tumor T13 Sectors

Project description:The following CGH experiments were conducted on six sectors (S1-S6) from a single primary ductal carcinoma tumor (T13) 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 subpopulation was labeled with Cy5 and hybridized to an 85K Bgl2 ROMA Microarray. A normal reference male fibroblast was labeled with Cy3 as a control. Samples were dye-swapped and the experiments were conducted in color-reversal. The value data repesents a log ratio of the mean of two dye-swapped samples

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