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Chromatin immunoprecipitation of human HeLa cells grown under serum starved conditions to identify new target genes for ETS-domain transcription factor Elk-1

ABSTRACT: Chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip) was carried out to identify new target genes for ETS-domain transcription factor Elk-1. Experiment was done in Hela cells under serum starved conditions.

ORGANISM(S): Homo sapiens

SUBMITTER: Leo Zeef

PROVIDER: E-MEXP-2084 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery.

Boros Joanna J Donaldson Ian J IJ O'Donnell Amanda A Odrowaz Zaneta A ZA Zeef Leo L Lupien Mathieu M Meyer Clifford A CA Liu X Shirley XS Brown Myles M Sharrocks Andrew D AD

Genome research 20090817 11

Transcription factors play an important role in orchestrating the activation of specific networks of genes through targeting their proximal promoter and distal enhancer regions. However, it is unclear how the specificity of downstream responses is maintained by individual members of transcription-factor families and, in most cases, what their target repertoire is. We have used ChIP-chip analysis to identify the target genes of the ETS-domain transcription factor ELK1. Two distinct modes of ELK1 ...[more]

PMID: 19687146

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Chromatin immunoprecipitation of human Hela cells grown under serum starved condtions to identify new targets genes for ETS-domain transcription factor Elk-1

Project description:Chromatin immunoprecipitation coupled with microarray analysis (ChIP-chip) was carried out to identify new target genes for ETS-domain transcription factor Elk-1. Experiment was done in Hela cells under serum starved conditions.

2009-08-11 | E-MEXP-1527 | biostudies-arrayexpress

16MB binding of H3ac, H4ac, STAT1, IRF1 antibodies in IFNg treated and untreated HeLa cells using nimblegen array

Project description:Analysis of H3ac, H4ac, STAT1 and IRF1 binding in IFNg treated and untreated HeLa cells for 6 hours was done using 50mer oligonucletide probes at 30bp intervals tiling over non-repetitive 16MB gene locus(HG17) Keywords: ChIP-chip three replicates for each marker at each state.

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Project description:This series includes 3 microarrays used to detect SWCoV1, a novel group III coronavirus in Delphinapterus leucas (Beluga whale) liver. The series includes 2 control whale livers and 1 whale liver containing SWCoV1.

2008-04-15 | E-GEOD-9238 | biostudies-arrayexpress

Chromatin immunoprecipitation with p53-antibody of human osteosarcoma cell line Saos-2 infected with adenomviruses encoding GFP, or GFP with p53 H1 helix mutants EL or RE

Project description:ChIP-chip study using Saos-2 cell line infected with adenoviruses encoding GFP (Mock) or GFP together with the p53 H1 helix mutants EL or RE. DNA-protein-complexes were precipitated with monoclonal p53-antibody (clone DO-1). Mock-chromatin was immunoprecipitated in the absence of antibody.<br>Three completely independent biological replicates were performed for each antibody, obtaining the corresponding input as total genomic DNA reference. Hybridizations were performed using Affymetrix GeneChip Human Tiling 2.0R Array set (7 arrays set).<br><br> Affymetrix .BAR files and an additional processed data file containing the coordinates of the identified binding sites can be found in the FTP directory for this experiment. <A HREF="ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/MEXP/E-MEXP-1748">FTP directory</A>

2010-05-13 | E-MEXP-1748 | biostudies-arrayexpress

ChIP-Seq with anti-FLAG antibodies to determine binding of LexA-3xFLAG to DNA in Streptomyces venezuelae treated with Mitomycin C (MMC) overnight

Project description:LexA is a transcriptional repressor for genes requiring expression primarily during SOS response in response to stress such as that caused by DNA alkylating agent Mitomycin C (MMC). LexA undergoes self-cleavage under stress conditions thereby lifting the repression on genes whose expression is required for stress response. In our experiment LexA binding sites in the genome were determined in untreated and MMC treated (overnight, 14h) cultures using a LexA-3xFLAG strain and anti-FLAG monoclonal antibodies. Wild type Streptomyces venezuelae (unFLAGged LexA) cultures, with and without MMC treatment were used as negative controls.

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Genetic Structure of Duplicated Sequences Revealed by Genotyping Single Sperm

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2008-07-25 | E-GEOD-11957 | biostudies-arrayexpress

ChIPseq of IMR32 cells treated with ISX or solvent control

Project description:IMR32 cells were treated with DMSO/ISX and Histone code and MycN binding was assessed via ChIPseq.

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Identification by ChIP-Seq of the binding sites of the extracytoplasmic function (ECF) sigma factor SigE in the genome of Streptomyces coelicolor A3(2) M600.

Project description:SigE is a sigma factor found in Streptomyces species and is the key regulator of cell envelope stress response in Streptomyces coelicolor. This ChIP-Seq experiment was carried out to determine the binding sites of SigE under conditions of cell envelope stress induced by 10 ug / ml vancomycin for 30 minutes. A 3xFLAG tagged SigE was introduced in a SigE deletion strain and ChIP-Seq was carried out using M2 (Sigma Aldrich A2220) gel suspension. Non-immunoprecipitated (total) DNA preparations were used for background determination and the wild type M600 was used as the negative control.

2019-04-24 | E-MTAB-7827 | biostudies-arrayexpress

Chromatin Affinity Precipitation-chiop of B. subtilis to gain insight into the invivo dynamics of RNA polymerase

Project description:To obtain an insight into the in vivo dynamics of RNA polymerase (RNAP) on the B. subtilis genome, we analyzed the distribution of ?A and ? subunits of RNAP and the NusA elongation factor on the genome in exponentially growing cells, using the ChAP (Chromatin Affinity Precipitation)-chip method. In contrast to E. coli RNAP, which often accumulates at the promoter-proximal region, B. subtilis RNAP is evenly distributed from the promoter to the coding sequences in the majority of genes. This finding suggests that B. subtilis RNAP recruited to the promoter promptly translocates away from the promoter to form the elongation complex. We detected RNAP accumulation in the promoter-proximal regions of some genes, most of which are attributed to transcription attenuation systems in the leader region. Our findings suggest that the differences in RNAP behavior during initiation and early elongation steps between E. coli and B. subtilis result in distinct strategies for post-initiation control of transcription. The E. coli mechanism involves trapping at the promoter and promoter-proximal pausing of RNAP in addition to transcription attenuation, whereas transcription attenuation in leader sequences is mainly employed in B. subtilis. Wild-type strain, Bacillus subtilis 168, was also used for RNA and genomic DNA extraction and analysis - RNA data was divided by genome DNA data to normalize (1) PCR bias and (2) copy number of RNA molecule per genome for multi-copy genome of exponentially growing bacteria.

2010-06-29 | E-MEXP-2649 | biostudies-arrayexpress