Filter Results
1187 results
  • Accession Number: GSE83408 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2016-12-05 Summary: 80% of the genomic binding sites of the histone acetyltransferase Gcn5 are colocalizing with CP190 binding. Depletion of CP190 reduces the number of Gcn5 binding sites and binding strength to chromatin. Binding dependency was further supported by Gcn5 mediated co-precipitation of CP190 Overall Design: Gcn5 ChIP-Seq in Kc cells treated either with GFP RNAi or CP190 RNAi Contact: Name: Marek Bartkuhn Organization: Justus-Liebig-University Giessen Deparment: Institute for Genetics Address: Heinrich-Buff-Ring 58 Giessen Hessen 35392 Germany Email: marek.bartkuhn@gen.bio.uni-giessen.de Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE64464 Platform: GPL14601: AB SOLiD 4 System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-11-06 Summary: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. We have generated CBP ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data. This shows that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb Response Elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. Overall Design: ChIP seq in Drosophila S2 cells using two different antibodies against CBP (nejire), one raised in rabbit against amino acids 2540-3190 (CBP rb), and one raised in guinea-pig against amino acids 1-178 (CBP gp) Contact: Name: Mattias Mannervik Organization: Stockholm University Laboratory: Mattias Mannervik Deparment: Molecular Biosciences, the Wenner-Gren Institute Address: Arrheniuslaboratories E3 Stockholm 10691 Sweden Email: mattias.mannervik@su.se Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE48621 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-07-23 Summary: We have conducted ChIP-Seq of H3K4me1/H3K27ac in order to perform a comparative study between wing imaginal discs and eye imaginal discs from Drosophila melanogaster. Overall Design: Examination of two histone modifications associated with gene regulation in wing/eye imaginal discs cells Contact: Name: Enrique Blanco Organization: Center for Genomic Regulation (CRG) Laboratory: Epigenetic Events in Cancer (L. Di Croce's lab) Deparment: Gene Regulation, Stem Cells and Cancer Address: Dr. Aiguader 88 Barcelona 08003 Spain Email: enrique.blanco@crg.eu Phone: +34 93 316 01 00 Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE20890 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-03-16 Summary: modENCODE_submission_2783 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-seq Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Antibody Pan MCM2-7 Antibody Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE20889 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-03-16 Summary: modENCODE_submission_2755 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-seq Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: Kc167; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Genotype: se/e; Sex: Female; EXPERIMENTAL FACTORS: Antibody dORC2 Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA
    Data Types:
    • Text
  • No Redistribution of Pol II over Transposons Is Observed in piwi Mutant Files (A) Scatterplot displaying Pol II ChIP-seq RPM values versus input RPM values over consensus transposable elements in wild-type and piwi mutant flies. (B) Shown are Pol II ChIP-seq and input RPM levels over the transposon consensus sequences of F-element and mdg3. ... The Huang et al. Data Processing Pipeline Generates Artificial Enrichment over Repetitive Regions The Piwi ChIP-seq and input/background datasets were processed following the Huang et al. pipeline (”Piwi ChIP”). In addition, the pipeline was also run swapping the ChIP and the input, i.e., the control sample was treated as ChIP and vice versa, resulting in the “background” track. (A) The fraction of signal mapping to transposable elements was calculated, revealing higher “enrichment” in the background than in the Piwi ChIP-seq dataset. (B) Strong apparent enrichment over individual transposable elements was observed in the ChIP track (upper track), as reported by Huang et al., but also in the background track (lower track), and even over different portions of the same transposable element in both tracks (middle track), strongly arguing that the enrichment over transposable elements reported by Huang et al. is a computational artifact. Signal observed on individual copies correlates well with enrichment profiles when mapped to the consensus sequence of the respective transposons (shown below each track). Sequences showing “enrichment” in the background are indicated with gray blocks to depict the correlations between the signal on individual TE copies and the consensus sequence. (C) Fraction of signal (calculated with the Huang et al. pipeline) mapping to transposable elements for the modENCODE transcription factor set. ... Piwi Is Not Enriched over Transposons in the Huang et al. Dataset (A) Absence of enrichment in the Piwi ChIP-seq dataset and high enrichment of H3K9me3 (from Muerdter et al., 2013) over consensus transposons; each dot corresponds to a transposon consensus sequence. (B) The concentration of Piwi signal over transposons in the Huang et al. dataset arises from failure to normalize multiply mapping reads. Shown is the region from Figure 2C of Huang et al. (2013). Top: Piwi ChIP-seq and background (input) data from Huang et al. showing (1) unique alignments; (2) all alignments, with reads normalized for mapping multiplicity; and (3) all alignments, with each alignment treated as a uniquely mapped read. Bottom: data processed per Huang et al. The enrichment of Piwi over repetitive elements is only observed when no multi-read normalization is applied and is seen in both ChIP and control datasets. (C) The minimal Piwi ChIP-seq enrichment observed over some individual transposable elements is well within the range of experimental noise. Shown is the cumulative distribution function (CDF) of the ratio between total ChIP RPM and control/background RPM for each DNA, LINE, or LTR repetitive element (each dot represents an individual TE insertion). Piwi ChIP-seq data from Huang et al. (red) and H3K9me3 data from Muerdter et al. (blue) are plotted alongside the cumulative distribution for 11 transcription factor ChIP-seq datasets from modENCODE (gray), for which there is no expectation of enrichment at repetitive elements. Only repeat instances with at least 10 RPM in at least one of the ChIP and control datasets for each ChIP/background pairing were included. H3K9me3 showed high average enrichment over background at most of the elements in all three classes. In contrast, the Piwi ChIP-seq data were well within the range of the distributions for modENCODE transcription factors.
    Data Types:
    • Image
    • Document
  • Accession Number: GSE20887 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-03-16 Summary: modENCODE_submission_2753 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: CHIP-seq Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: S2-DRSC; Tissue: embryo-derived cell-line; Developmental Stage: late embryonic stage; Sex: Male; EXPERIMENTAL FACTORS: Antibody dORC2 Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE37864 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-12-11 Summary: ChIP-Seq profiles of MSL1, MSL2, MSl3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 in Drosophila S2 cells Overall Design: MSL1, MSL2, MSL3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 ChIP in Drosophila S2 cells. 1-3 biological replicates per experiment. Performed in single-read and paired-end read mode. Contact: Name: Tobias Straub Organization: LMU Munich Deparment: Biomedical Center, Bioinformatics Address: Großhadener Str. 9 Martinsried 82152 Germany Email: tstraub@med.uni-muenchen.de Organization: GEO Address: USA
    Data Types:
    • Text
  • ChIP-Seq profiles of MSL1, MSL2, MSl3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 in Drosophila S2 cells MSL1, MSL2, MSL3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 ChIP in Drosophila S2 cells. 1-3 biological replicates per experiment. Performed in single-read and paired-end read mode.
    Data Types:
    • Text
  • Accession Number: GSE36404 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-02-06 Summary: see Super Series Summary Overall Design: Cross-linked chromatin derived from Drosophila S2-DRSC cells was immunoprecipitated using antibodies targeting ASH1 and FSH. Precipitated chromatin was sequenced applying Illumina sequencing. Contact: Name: Tobias Kockmann Organization: ETHZ Laboratory: Paro Deparment: D-BSSE Address: Mattenstr. 26 Basel Switzerland Email: tobias.kockmann@bsse.ethz.ch Organization: GEO Address: USA
    Data Types:
    • Text
11