Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Suz12 target promoters in Ntera, MCF7 and SW480 cells

ABSTRACT: For each sample a matched total was produced in parallel. Amplicons were made from each and hybridized on human 5.0 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

ORGANISM(S): Homo sapiens

PROVIDER: GSE4905 | GEO | 2006/06/06

SECONDARY ACCESSION(S): PRJNA95929

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Oct4 and RNA Pol II target promoters in Ntera cells

Project description:These samples are biological replicates from Ntera cells that were crosslinked on different days. For each sample a matched total was produced in a parallel. Amplicons were made from each and hybridized on human 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

2006-06-06 | GSE4904 | GEO

Suz12, EZH2, EED1, H3me3K27, H3me3K9 and RNA Pol II target promoters in mouse F9 and mES cells

Project description:For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

2006-06-06 | GSE4908 | GEO

Suz12, EZH2, EED1, H3me3K27 binding sites in Ntera cells

Project description:All samples are from the same batch of crosslinked Ntera cells with a matched total produced in parallel. Amplicons were made from each and hybridized on ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip

2006-06-06 | GSE4902 | GEO

Suz12, EZH2 and H3me3K27 binding sites in F9 cells

Project description:Suz12 samples are biological replicates from F9 cells crosslinked on different days. EZH2 and H3me3K27 samples are from the same batch of crosslinked cells as Suz12 replicate 2. For each sample matched total was prepared in parallel. Amplicons were made and hybridized on custom genomic tiling arrays. Keywords: ChIP-chip

2006-06-06 | GSE4907 | GEO

HeLa E2F1 ChIP-chip experiments

Project description:These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Goal was determination of E2F1 binding sites in HeLa cells by using ChIP-chip methodology. See Farnham Lab website for downloadable protocol for ChIP or supplementary file (Chip_protocol.txt) below. NimbleGen performed all array processing. See NimbleGen website for information on array procedures.

2010-07-01 | E-GEOD-4306 | biostudies-arrayexpress

HeLa E2F1 ChIP-chip experiments

2006-02-28 | GSE4306 | GEO

Dynamics of 5-hydroxymethylcytosine and chromatin marks in mammalian neurogenesis

Project description:H3K36me3 (ChIp-ChIp), H3K4me3 (ChIp-ChIp), H3K27me3 (ChIp-ChIp), 5mC (MIRA) and 5hmC (hMeDIP) profiles were analyzed in neural progenitor cells (NPC) and neurons by using Nimblegen Mouse ChIP-chip 2.1M Economy Whole-Genome Tiling - 4 Array Set. In order to compare two different techniques of 5hmC profiling, we performed 5hmC profiling with Hydroxymethyl Collector™ Kit (Active Motif) method and hybridized it on mouse Chr7 fragment (Nimblegen). As an independent experiment, 5hmC profiling was performed by using hMeDIP method and hybridized on mouse Chr7 fragment (Nimblegen). After MIRA enrichment and genome amplification, DNA was hybridized on mouse Chr7 fragment (Nimblegen).

2012-12-31 | GSE38118 | GEO

Mus musculus

Project description:ChIP-chip on custom NimbleGen genomic tiling arrays

| PRJNA105111 | ENA

AML1/ETO binding pattern on human promoters

Project description:Approximately 20% of Acute Myelogenous Leukemia (AML) cases carry the t(8;21) translocation, which involves the AML1 and ETO genes, and express the resulting AML1/ETO fusion protein that functions as a transcriptional repressor by recruiting NCoR/SMRT/HDAC complexes to DNA. We used microarrays to identify human promoters bound by AML1/ETO in U937 cells. Keywords: ChIP-chip A U937 cell line that conditionally expresses HA-tagged AML1/ETO under the control of the mouse metallothionine promoter (U937-A1E) (Alcalay et al., J.Clin.Invest, 2003,112, 1751-1761) was used. Cells were treated for 8h with 100uM ZnSO4 to induce transgene expression, and ChIP was performed using an anti-HA antibody. ChIP products were then PCR amplified, labeled with Cy3/Cy5 fluorescent dyes and hybridized to the NimbleGen HG17 Human Promoter 2 Array set, which explores 4 kb upstream and 1 kb downstream the transcription start site (TSS) of 24,434 annotated genes. Two biological replicates were prepared and hybridized to independent array sets. U937-Mt cells, which carry the empty vector, served as control for non-specific binding of the anti-HA antibody.

2008-12-21 | E-GEOD-10531 | biostudies-arrayexpress

Extrachromosomal circular SUZ12 amplicon dictates retinoblastoma progression through reprogramming H3K27 methylation [eccDNA-seq]

Project description:Extrachromosomal circular DNA (eccDNA) is double-stranded circular DNA that is derived from but independent of chromosomal DNA. Owing to its nonchromosomal inheritance, eccDNA facilitates the amplification of oncogenes and expedites the process of genome evolution in tumor. However, the role of eccDNA in RB remains enigmatic. We combined Circle-Seq and RNA-Seq to identified crucial extrachromosomal circular oncogene amplicons. Herein, we revealed that extrachromosomal circular SUZ12 amplicon regulates H3K27me3 modification during the oncogenic progression of retinoblastoma. Conclusively, our study initially delineated an integrated picture of the eccDNA landscape in retinoblastoma and unveiled a novel SUZ12-containing eccDNA/H3K27me3 oncogenic mechanism where eccDNA dictates retinoblastoma progression through regulating transcription levels of linear DNA.

2023-07-02 | GSE235888 | GEO

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