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  • Accession Number: GSE16013 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2009-05-12 Summary: This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-seq data generated on Solexa Genome Analyzer for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. Keywords: Epigenetics For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure. Contact: Name: Kevin P. White Organization: University of Chicago Deparment: Institute for Genomics and Systems Biology Address: 900 E. 57th STR. 10th FL. Chicago IL 60615 USA Email: kpwhite@uchicago.edu Organization: GEO Address: USA
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  • Accession Number: GSE59726 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-10-13 Summary: This submission data was generated in Angela Stathopoulos's lab. Project goal was to map Su(H) associated regions on Drosophila melanogaster genome. In Drosophila embryos, a nuclear gradient of Dorsal (Dl) directs differential gene expression along the dorsoventral (DV) axis, translating it into distinct domains separated by sharp boundaries between future mesodermal, neural and ectodermal territories. However, the mechanisms used to differentially position gene expression boundaries along this axis are not fully understood. Here, we show that the transcription factor Suppressor of Hairless [Su(H)] influences the positioning of dorsal boundaries for many genes expressed along the DV axis. Synthetic reporter constructs provide molecular evidence that Su(H) binding sites support repression and act to counterbalance activation through Dl and the ubiquitous activator Zelda. Overall, our study highlights a role for broadly expressed repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory modules as important elements controlling spatial domains of gene expression, to facilitate flexible positioning of boundaries across the entire DV axis. Overall Design: 1 g of 2-4 hour yw embryos were used. Two replicate ChIP-seq samples were analyzed using goat (Santa cruz goat polyclonal #sc-15813), and rabbit (Santa cruz rabbit polyclonal #sc-25761) antibodies. Contact: Name: Angelike Stathopoulos Organization: California Institute of Technology Deparment: Biology and Biological Engineering Address: 1200 E. California Blvd - MC114-96 Pasadena CA 91125 USA Email: angelike@caltech.edu Organization: GEO Address: USA
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  • Accession Number: GSE39393 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-11-25 Summary: Here we report the identification of genomic regions of DNA bound by Dp1 in Drosophila S2R+ cells. Dp1 is a dimerization partner of several E2F transcription factors and is needed for E2F target promoter binding. We find that Dp1 binds the promoter regions of genes important for oxidative phosphorylation. This result is important since our data demonstrates that expression of several oxidative phosphorylation genes is down-regulated in dDP mutant Drosophila 3rd instar larval eye imaginal discs. These ChIP-seq results suggest that the mechanism by which dDP regulates expression of these genes is direct. In addition, we have confirmed a number of these Dp1 bound gene promoters by conventional Chromatin Immunoprecipitation. Overall Design: Examination of Dp1 bound regions of genomic DNA in S2R+ cells. Contact: Name: Elizaveta V Benevolenskaya Organization: University of Illinois at Chicago Deparment: Biochemistry and Molecular Genetics Address: 900 S. Ashland Ave. Chicago IL 60607 USA Email: evb@uic.edu Phone: 312-413-8947 Organization: GEO Address: USA
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  • Accession Number: GSE60428 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) GPL15872: Illumina Genome Analyzer IIx (Drosophila yakuba) GPL15873: Illumina Genome Analyzer IIx (Drosophila virilis) GPL17484: Illumina Genome Analyzer IIx (Drosophila simulans) GPL17883: Illumina Genome Analyzer IIx (Drosophila pseudoobscura) Organism: Drosophila melanogaster Published on 2014-10-20 Summary: We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter Overall Design: ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species Contact: Name: Bernd Schuettengruber Organization: Institute de Génétique Humaine Laboratory: Cavalli Address: 141, rue de la cardonille Montpellier 34396 France Email: bernd.schuttengruber@igh.cnrs.fr Organization: GEO Address: USA
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  • Accession Number: GSE20888 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-03-16 Summary: modENCODE_submission_2754 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: ML-DmBG3-c2; Tissue: CNS-derived cell-line; Developmental Stage: third instar larval stage; Genotype: y v f mal; Sex: Unknown; 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
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  • Accession Number: GSE55932 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-11-10 Summary: We analyzed gamma-H2Av ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from wild-type (OrR) or suppressor of under-replication (SuUR) mutant Drosophila. Goals were to determine the DNA damage profile relative to underreplicated domains. We analyzed SUUR and Cdc45 ChIP-Seq from hand dissected early (stage 10) and late (stage 12/13) egg chambers from adult Drosophila ovaries. The goals was to determine the localization of SUUR relative to replication forks. Overall Design: ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila, analyzed by Illumina sequencing. One replicate is included for each of OrR (WT) or SuUR salivary glands.Rabbit IgG controls are included for OrR (WT). ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers, analyzed by Illumina sequencing. One replicate is included for each ChIP reaction. Contact: Name: Terry L. Orr-Weaver Organization: Whitehead Institute for Biomedical Research Laboratory: Orr-Weaver Address: 9 Cambridge Center Cambridge MA 02142 USA Email: weaver@wi.mit.edu Phone: 617-258-5251 Organization: GEO Address: USA
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  • Accession Number: GSE36310 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-05-23 Summary: In order to idetify paused promoters in vivo, we performed tissue specific Pol II Chip-seq using mutant embryos for the dorsal gradient. We used two population of cells, either dorsal ectoderm cells (gd7 embryos) or mesodermal cells (Toll10b) embryos. Overall Design: ChIP-seq for Pol II in various Drosophila embryos Contact: Name: Julia Zeitlinger Organization: Stowers Institute for Medical Research Laboratory: Zeitlinger Lab Address: 1000 E 50th St Kansas City MO 64110 USA Email: jbz@stowers.org Organization: GEO Address: USA
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  • Accession Number: GSE25709 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-12-04 Summary: ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2. ArrayExpress Release Date: 2010-04-16 Publication Title: The Nonspecific Lethal Complex Is a Transcriptional Regulator in Drosophila Publication Author List: Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, Akhtar A. Person Roles: submitter Person Last Name: Vaquerizas Person First Name: Juan Person Mid Initials: M Person Email: jvaquerizas@ebi.ac.uk Person Phone: Person Address: Person Affiliation: EBI Overall Design: Experimental Design: individual_genetic_characteristics_design Experimental Design: in_vivo_design Experimental Design: binding_site_identification_design Experimental Design: ChIP-seq Experimental Factor Name: CHIP-ANTIBODY Experimental Factor Type: Chip-antibody Contact: Name: ArrayExpress EBI Organization: European Bioinformatics Institute Laboratory: ArrayExpress Address: Wellcome Trust Genome Campus Hinxton Cambridgeshire United Kingdom Email: miamexpress@ebi.ac.uk Organization: GEO Address: USA
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  • Accession Number: GSE37032 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-08-02 Summary: Chromatin profiling of nuclei isolated from genetically defined neuronal subpopulations of the adult Drosophila brain. Overall Design: Cell type-specific histone modification maps were generated from nuclei isolated from all neurons (R57C10-GAL4), Kenyon cells (OK107-GAL4), and octopaminergic (Tdc2-GAL4) neurons using a method similar to INTACT (Deal and Henikoff, 2010; Steinner et al., 2012). Three histone modifications were profiled: H3K4me3, H3K27ac, and H3K27me3. Sequencing was performed with an Illumina HiSeq 2000. Contact: Name: Fred P Davis Organization: HHMI Janelia Farm Research Campus Address: 19700 Helix Dr Ashburn VA 20147 USA Email: davisf@janelia.hhmi.org Phone: 571-209-4000-3437 Organization: GEO Address: USA
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  • This SuperSeries is composed of the following subset Series: GSE33546: Polycomb repressive complex 2-dependent and –independent functions of Jarid2 in transcriptional regulation in Drosophila [ChIP-Seq] GSE36038: Polycomb repressive complex 2-dependent and –independent functions of Jarid2 in transcriptional regulation in Drosophila [Affymetrix] Refer to individual Series
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