Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

67 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin immunoprecipitation of trimethylated histone H3-K27 in human prostate cancer cell line PC3

ABSTRACT: Epigenetic silencing in cancer cells is mediated by at least two distinct histone modifications, polycomb based histone H3 lysine 27 trimethylation (H3K27triM) and H3K9 dimethylation.

Using chromatin immunoprecipitation-microarrays (ChIP-chip) in prostate cancer cells, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM. These genes were silenced specifically in prostate cancer, and those CpG islands affected showed low levels of DNA methylation.

ORGANISM(S): Homo sapiens

DISEASE(S): prostate cancer

SUBMITTER: Yutaka Kondo

PROVIDER: E-MEXP-1585 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP_Glioma_stem cells

Project description:To examine profiles of K4me2 and K27me3 in glioma stem cells

2011-08-31 | E-TABM-1120 | biostudies-arrayexpress

ChIP-chip profiling of rat normal and failed hearts of Dahl strain

Project description:Left ventricle myocytes from Dahl rats with a normal or failed heart was subjected to mRNA quantitation or ChIP-on-chip experiments with Affymetrix Rat Genome 230 2.0 microarrays. Experiment Overall Design: One left venctricle specimen was used for each mRNA quantitation/ChIP-on-chip experiment with a normal or failed heart.

2009-03-01 | E-GEOD-8341 | biostudies-arrayexpress

Chromatin immunoprecipitation of wild type msc1D and swr1D fission yeast to determine genome-wide distribution of H2A.Z

Project description:Eukaryotic genomes are repetitively packaged into chromatin by nucleosomes, however they are regulated by the differences between nucleosomes, which establish various chromatin states. Replication-independent histone exchange could potentially perturb chromatin status if histone exchange chaperones, such as Swr1C, loaded histone variants into wrong sites. Here we use ChIP-chip analysis of H2A.Z-myc to show that in S.pombe, like S.cerevisiae, Swr1C is required for loading H2A.Z into specific sites, including the promoters of lowly expressed genes. However S.pombe Swr1C has an extra subunit, Msc1, which is a JumonjiC-domain protein of the Lid/Jarid1 family. The absence of Msc1 does not disrupt the S.pombe Swr1C or H2A.Z distribution in euchromatin. However in the absence of either Msc1 or Swr1 H2A.Z is ectopically found in the inner centromere and in subtelomeric chromatin. Normally this subtelomeric region, which appears to be a novel chromatin domain that we term ST-chromatin, not only lacks H2A.Z but also shows uniformly lower levels of H3K4me2, H4K5 and K12K5 acetylation than euchromatin. It also disproportionately contains the most lowly expressed genes during vegetative growth, including many meiotic-specific genes. These data describe H2A.Z distribution in S.pombe and identify a new mode of chromatin surveillance and maintenance based on negative regulation of histone variant misincorporation.

2009-11-09 | E-MEXP-1986 | biostudies-arrayexpress

ChIP-chip by array of mouse haematopoietic and endothelial cell lines using an anti-H3 trimethyl lysine 4 antibody

Project description:chromatin immunoprecipitations were performed in mouse haematopoietic and endothelial cell lines using an anti-H3 trimethyl lysine 4 antibody

2011-09-06 | E-MEXP-2908 | biostudies-arrayexpress

Transcription profiling by array of mouse bone marrow proB cells treated with IL-7 or CpG

Project description:Culture of proB cells with IL7 in the presence or absence of CpG

2010-02-27 | E-MEXP-2595 | biostudies-arrayexpress

ChIP-chip by array of mouse 416Bcell line using anti-PU.1 (Santa Cruz, sc-352X).

Project description:Immunoprecipitations were performed using anti-PU.1 (Santa Cruz, sc-352X)

2011-04-07 | E-MEXP-2666 | biostudies-arrayexpress

ChIP-chip by array of mouse cell lines and fresh tissue using anti-acetyl histone H3 antibody.

Project description:Immunoprecipitations were performed using anti-acetyl histone H3 antibody (Millipore, 06-599)

2011-04-07 | E-MEXP-2664 | biostudies-arrayexpress

ChIP-chip by array of mouse cell lines and fresh tissues using anti-H3 trimethyl lysine 4.

Project description:Immunoprecipitations were performed using anti-H3 trimethyl lysine 4 (Millipore, 04-745 and gift from Dr. L. OM-oM->M-^RNeill, Birmingham, UK)

2010-06-09 | E-MEXP-2665 | biostudies-arrayexpress

The FUN30 Chromatin Remodeler Fft3 Protects Centromeric and Subtelomeric Domains from Euchromatin Formation

Project description:The chromosomes of eukaryotes are organized into structurally and functionally discrete domains. This implies the presence of insulator elements that separate adjacent domains, allowing them to maintain different chromatin structures. We show that the Fun30 chromatin remodeler, Fft3, is essential for maintaining a proper chromatin structure at centromeres and subtelomeres. Fft3 is localized to insulator elements and inhibits euchromatin assembly in silent chromatin domains. In its absence, euchromatic histone modifications and histone variants invade centromeres and subtelomeres, causing a mis-regulation of gene expression and severe chromosome segregation defects. Our data strongly suggest that Fft3 controls the identity of chromatin domains by protecting these regions from euchromatin assembly.

2011-04-02 | E-MEXP-3044 | biostudies-arrayexpress

miR-126-126star in melanoma cell lines

Project description:Based on microRNA expression profiling studies, here we focus on miR-126&126* as the most downmodulated microRNAs in a panel of melanoma cell lines at different stages of progression compared with normal human melanocytes. At present no data exist on miR-126&126* possible role in melanoma. Our results show miR-126/miR-126* downregulation associated with tumor progression and the antineoplastic role deriving from their restored expression in metastatic melanomas in vitro as well as in vivo.

2013-05-21 | E-MEXP-3629 | 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