Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

92 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Methylation profiling of normal and cancerous breast cells from human patients and cell lines in a 125 kB region of the HOXA cluster

ABSTRACT: To evaluate DNA methylation profile associated with breast cancer in 125 kB region of HOXA cluster we analyzed DNA from normal cancerous breast specimens and cell lines. Analysis was performed on the tiling array covering entire HOXA region with 500bp resolution. Immunoprecipitation with anti-methylcytosine antibody was for target preparation. Cy3 labeling was used for inmmunoprecipitated DNA, Cy5 labeling was used for reference input DNA.

INSTRUMENT(S): GenePix 4000B [Axon Instruments]

ORGANISM(S): Homo sapiens

DISEASE(S): infiltrating ductal carcinoma

SUBMITTER: Taylor Jensen

PROVIDER: E-MEXP-880 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Epigenetic inactivation of the HOXA gene cluster in breast cancer.

Novak Petr P Jensen Taylor T Oshiro Marc M MM Wozniak Ryan J RJ Nouzova Marcella M Watts George S GS Klimecki Walter T WT Kim Christina C Futscher Bernard W BW

Cancer research 20061106 22

Using an integrated approach of epigenomic scanning and gene expression profiling, we found aberrant methylation and epigenetic silencing of a small neighborhood of contiguous genes-the HOXA gene cluster in human breast cancer. The observed transcriptional repression was localized to approximately 100 kb of the HOXA gene cluster and did not extend to genes located upstream or downstream of the cluster. Bisulfite sequencing, chromatin immunoprecipitation, and quantitative reverse transcription-PC ...[more]

PMID: 17090521

Similar Datasets

Methylation profiling of normal and cancerous human breast samples

Project description:To assess changes in DNA methylation state associated with breast cancer we analyzed DNA from normal and cancerous breast specimens on CpG islands microarray using methylation-sensitive enzyme McrBC for target preparation. Cy3 was used for McrBC cut sample, Cy5 was used for reference Mock sample.

2006-11-03 | E-MEXP-881 | biostudies-arrayexpress

Methylation profiling of different stages of human mammary epithelial cells from pre-statis to cancer

Project description:To characterize early epigenetic events in breast carcinogenesis, we analyzed DNA methylation state of different stages of HMECs from pre-stasis to cancer cell lines using human promoter microarray

2009-01-01 | E-MEXP-1889 | biostudies-arrayexpress

Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization

Project description:The secondary genetic events associated with follicular lymphoma (FL) progression are not well defined. We applied genome-wide BAC array comparative genomic hybridization to 106 diagnostic biopsies of FL to characterize regional genomic imbalances. Using an analytical approach that defined regions of copy number change as intersections between visual annotations and a Hidden Markov model-based algorithm, we identified 71 regional alterations that were recurrent in â?¥10% of cases. These ranged in size from ~200 kb to 44 Mb, affecting chromosomes 1, 5, 6, 7, 8, 10, 12, 17, 18, 19, and 22. We also demonstrated by cluster analysis that 46.2% of the 106 cases could be sub-grouped based on the presence of +1q, +6p/6q-, +7 or +18. Survival analysis showed that 21 of the 71 regions correlated significantly with inferior overall survival (OS). Of these 21 regions, 16 were independent predictors of OS using a multivariate Cox model that included the International Prognostic Index (IPI) Score. Two of these 16 regions (1p36.22-p36.33 and 6q21-q24.3) were also predictors of transformation risk and independent of IPI. These prognostic features may be useful to identify high-risk patients as candidates for risk-adapted therapies. Array comparative genomic hybridization analysis of 106 follicular lymphoma diagnostic biopsies

2010-05-25 | E-GEOD-12393 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection

Project description:This SuperSeries is composed of the following subset Series: GSE15746: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1 GSE15747: Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2 Refer to individual Series

2010-05-19 | E-GEOD-15801 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 2

Project description:Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. We have developed a method to profile genome wide methylation. 7 ovarian normal samples and 11 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method.

2010-05-19 | E-GEOD-15747 | biostudies-arrayexpress

Methylation detection Oligonucleotide Microarray Analysis: high resolution method for CpG island methylation detection 1

Project description:Methylation of CpG islands associated with genes can affect the expression of the proximal gene, and methylation of non associated CpG islands correlates to genomic instability. This epigenetic modification has been shown to be important in many pathologies, from development and disease to cancer. We report the development of a novel high-resolution microarray that detects the methylation status of over 25,000 CpG islands in the human genome. Experiments were performed to demonstrate low system noise in the methodology and that the array probes have a high signal to noise ratio. Methylation measurements between different cell lines were validated demonstrating the accuracy of measurement. We then identified alterations in CpG islands, both those associated with gene promoters, as well as non-promoter associated islands in a set of breast and ovarian tumors. We demonstrate that this methodology accurately identifies methylation profiles in cancer and in principle it can differentiate any CpG methylation alterations and can be adapted to analyze other species. We have developed a method to profile genome wide methylation. 12 breast normal samples and matching tumors from these individuals and an additional 28 tumor samples from other individuals were analyzed for CpG methylation. After inter array normalization, the tumor samples were taken together and the methylation compared to that of the normal samples to identify regions of the CpG islands that are significantly altered between the two datasets. Some of these regions were validated for their methylation as a proof of principle for the method.

2009-04-28 | E-GEOD-15746 | biostudies-arrayexpress

Transcription profiling of Rhizobium leguminosarum supressor strain RU2386 and gltb mutant compared to the wild type

Project description:Comparison of supressor strain RU2386 and gltB mutant (RU2307) to wildtype 3841 of Rhizobium leguminosarum

2008-02-02 | E-MEXP-1404 | biostudies-arrayexpress

AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Antibody Arrays (L-507)]

Project description:Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this â??AKTlowâ?? cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication. Secreted protein profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated using antibody arrays.

2015-12-09 | E-GEOD-71892 | biostudies-arrayexpress

AKT Inhibition Promotes Non-autonomous Cancer Cell Survival [Antibody Arrays (L-493)]

Project description:Small-molecule inhibitors of AKT signaling are being in evaluated in patients with various cancer types, but have so far proven therapeutically disappointing for reasons that remain unclear. Here, we treat cancer cells with sub-therapeutic doses of Akti-1/2, an allosteric small molecule AKT inhibitor, in order to experimentally model pharmacologic inhibition of AKT signaling in vitro. We then apply a combined RNA, protein, and metabolite profiling approach to develop an integrated, multi-scale, molecular snapshot of this âAKTlowâ cancer cell state. We find that AKT-inhibited cancer cells suppress thousands of mRNA transcripts, and proteins related to the cell cycle, ribosome, and protein translation. Surprisingly, however, these AKT-inhibited cells simultaneously up-regulate a host of other proteins and metabolites post-transcriptionally, reflecting activation of their endo-vesiculo-membrane system, secretion of inflammatory proteins, and elaboration of extracellular microvesicles. Importantly, these microvesicles enable rapidly proliferating cancer cells of various types to better withstand different stress conditions, including serum deprivation, hypoxia, or cytotoxic chemotherapy in vitro and xenografting in vivo. These findings suggest a model whereby cancer cells experiencing a partial inhibition of AKT signaling may actually promote the survival of neighbors through non-cell autonomous communication. Secreted protein profiles of MCF7 and HCT116 Akti-1/2 treated cells and MCF7 and HCT116 vehicle (i.e. DMSO) treated cells were generated using antibody arrays.

2015-12-09 | E-GEOD-71891 | biostudies-arrayexpress

Mycobacterium tuberculosis whiB4 mutant expression

Project description:Comparison of gene expression profile of the whiB4 mutant strain of Mycobacterium tuberculosis with the wild type Mycobacterium tuberculosis H37RV Mtb WhiB4 mutant mRNA was compared with the mRNA of wtMtb H37RV under aerobic conditons Aerbic conditions OD600 nm of 0.4, MtbWhiB4KO vs wtMtb, biological replicates: 3 wt Mtb H37RV and 3 MtbWhiB4 KO

2012-07-23 | E-GEOD-37840 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data