Filter Results
575 results
  • Accession Number: GSE74413 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2016-08-02 Summary: The goal of this experiment was to identify genomic dCAP-D3 binding sites in Drosophila S2R+ cells Overall Design: dCAP-D3 was immunoprecipitated in two separate experiments with antibody YZ834 which was developed in the Longworth lab. IgG immunoprecipiation was performed alongside the dCAP-D3 immunoprecipitation to serve as controls for each experiment. Input chromatin was also harvested from each of the two experiments. Contact: Name: Michelle Suzanne Longworth Organization: Cleveland Clinic Foundation Laboratory: Longworth Deparment: Molecular Genetics Address: 9500 Euclid Ave NE20 Cleveland OH 44195 USA Email: longwom@ccf.org Phone: 216-618-6114 Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE63323 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-11-21 Summary: Alternative polyadenylation (APA) has been implicated in a variety of developmental and disease processes, such as stem cell differentiation and cancer. A particularly dramatic form of APA has been documented in the developing nervous system of flies and mammals, whereby a variety of neurogenic genes undergo coordinate extension of their 3’ UTRs. In Drosophila, the RNA-binding protein ELAV inhibits RNA processing at proximal polyadenylation (poly(A)) sites, thereby fostering the formation of 3’ extensions that can reach 12 kb in length. Here, we present evidence that paused Pol II plays an important role in the selective recruitment of ELAV to elongated genes. Replacing native promoters of elongated genes with heterologous promoters blocks normal 3’ extension in the nervous system, while native promoters can induce 3’ extension in ectopic tissues expressing ELAV. Computational analyses suggest that the promoter regions of elongated genes tend to contain paused Pol II and associated cis-regulatory elements such as GAGA. ELAV ChIP-Seq assays indicate pervasive binding to the promoter regions of extended genes. Our study provides the first evidence for a regulatory link between promoter-proximal pausing and APA. Overall Design: ELAV ChIP-Seq assays were conducted with nuclei obtained from 6-8 hr and 10-12 hr embryos Contact: Name: Wei Zhang Organization: UC Berkeley Address: University of California at Berkeley Berkeley 94720 USA Email: wzhang1984@gmail.com Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE51598 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-08-11 Summary: H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Overall Design: Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment 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: GSE52029 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-06-04 Summary: Here we use ChIP-seq in Drosophila embryos to determine the genome-wide binding pattern of TBP and Trf2 using two different antibodies for each factor. Overall Design: ChIP-seq using anti-Trf2 and anti-TBP antibodies in 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
    Data Types:
    • Text
  • Accession Number: GSE49511 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-10-30 Summary: We have used ChIP-seq on Drosophila S2 cells to characterize genome-wide DSX occupancy. Overall Design: We have perfomed ChIP-seq on S2 cells transfected with either V5-tagged DSXF or DSXM constructs. We performed three biological replicates for each ChIP sample and two biological replicates for the input samples. For peak calling and analysis, the reads from all biological replicates were pooled before aligning them to the genome. Contact: Name: Brian Oliver Organization: NIDDK, NIH Laboratory: Developmental Genomics Deparment: LCDB Address: 50 South Drive Bethesda MD 20892 USA Email: briano@helix.nih.gov Phone: 301-496-5495 Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE87471 Platform: GPL14762: AB SOLiD System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-03-16 Summary: We performed ChIP-seq with Drospohila Atrophin (also known as Grunge) antibody using S2 cell chromatin. Atro ChIP-seq peaks are most frequent in promoters and introns of highly expressed, paused genes in S2 cells, including several components of developmental signaling pathways. The Atro peaks overlap significantly with GAGA factor (Trithorax-like, Trl). Overall Design: ChIP-seq in Drosophila S2 cells with an antibody (4H6) raised against the peptide SRQSPLHPVP in the C-terminus of Drospohila Atro 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: GSE66689 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-06-18 Summary: We analyzed gamaH2Av ChIP-seq from hand dissected stage 10B and 13 follicle cell nuclei. Egg chambers were dissected from wild-type (OrR) or H2Av[ΔCT] ovaries to assess binding at the Drosophila Follicle Cell Amplicons and across the genome. Overall Design: ChIP-seq of gammaH2Av bound to follicle cell DNA from stage 10B and 13 egg chambers, collected from wild-type (OrR) and H2Av[ΔCT] Drosophila ovaries. Sequences analyzed by Illumina sequencing. Two replicates are 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
    Data Types:
    • Text
  • Accession Number: GSE82151 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2016-07-01 Summary: The patterning of Drosophila retina occurs both very fast and with high precision. This process is driven by the dynamic changes in signalling activity of the conserved Hedgehog (Hh) pathway, which coordinates cell fate determination, cell cycle and tissue morphogenesis. Here we show that during Drosophila retinogenesis, the retinal determination gene dachshund (dac) is not only a target of the Hh signaling pathway, but is also a modulator of its activity. Using developmental genetics techniques, we demonstrate that dac enhances Hh signaling by promoting the accumulation of the Gli transcription factor Cubitus interruptus (Ci) parallel to or downstream of fused. In the absence of dac, all Hh-mediated events associated to the morphogenetic furrow are delayed. One of the consequences is that, posterior to the furrow, dac- cells cannot activate a Roadkill-Cullin3 negative feedback loop that attenuates Hh signaling and which is necessary for retinal cells to continue normal differentiation. Therefore, dac is part of an essential positive feedback loop in the Hh pathway, guaranteeing the speed and the accuracy of Drosophila retinogenesis. Overall Design: ChIP-seq against Dachshund vs input ChIP-seq. Eye-antennal imaginal discs are dissected from Grh-GFP (Bloomington stock 42269) 3rd instar larvae and fixed with formaldehyde. Chromatin is prepared and sonicated until fragments reach an average size of 500 bp. Chromatin is immunoprecipitated with an anti-GFP Ab (ab290, Abcam) and the immunocomplexes are recovered with protein A/G magnetic beads (Millipore). Contact: Name: Jelle Jacobs Organization: KULeuven Laboratory: Lab of Computational Biology Deparment: Human Genetics Address: Herestraat 49 Leuven Belgium Email: jelle.jacobs@kuleuven.be Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE23542 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-10-25 Summary: Control of RNA transcription is critical for the development and homeostasis of all organisms, and can occur at multiple steps of the transcription cycle, including RNA polymerase II (Pol II) recruitment, initiation, promoter-proximal pausing, and elongation. That Pol II accumulates on many promoters in metazoans implies that steps other than Pol II recruitment are rate-limiting and regulated 1-6. By integrating genome-wide Pol II chromatin immunoprecipition (ChIP) and Global Run-On (GRO) genomic data sets from Drosophila cells, we examined critical features of Pol II near promoters. The accumulation of promoter-proximal polymerase is widespread, occurring on 70% of active genes; and unlike elongating Pol II within the body of genes, promoter Pol II are held paused by factors like NELF, unable to transcribe unless nuclei are treated with strong detergent. Notably, we find that the vast majority of promoter-proximal Pol II detected by ChIP are paused, thereby identifying the biochemical nature of this rate-limiting step in transcription. Finally, we demonstrate that Drosophila promoters do not have the upstream divergent Pol II that is seen so broadly and prominently on mammalian promoters. We postulate this is a consequence of Drosophila’s extensive use of directional core promoter sequence elements, which contrasts with mammals’ lack of directional elements and prevalence of CpG island core promoters. In support of this idea, we show that the fraction of mammalian promoters containing a TATA box core element is dramatically depleted of upstream divergent transcription. Overall Design: ChIP-seq data set for Pol II (rpb3) (2 replicates). Contact: Name: Leighton James Core Organization: Cornell University Laboratory: John T. Lis Deparment: Moleular Biology and Genetics Address: 417 Biotechnology Building Ithaca NY 14853 USA Email: ljc37@cornell.edu Organization: GEO Address: USA
    Data Types:
    • Text
  • Accession Number: GSE23544 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-10-12 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Comparison of multiple GRO-seq data sets and a ChIP-seq data set for Pol II (rpb3). GRO-seq also performed +/- Sarkosyl and after depletion of NELF by RNAi. Contact: Name: Leighton James Core Organization: Cornell University Laboratory: John T. Lis Deparment: Moleular Biology and Genetics Address: 417 Biotechnology Building Ithaca NY 14853 USA Email: ljc37@cornell.edu Organization: GEO Address: USA
    Data Types:
    • Text