Filter Results
1194 results
  • H3-ChIP-seq was performed in order to analyze changes in nucleosomal occupancy after depletion of CTCF/P190 and ISWI from Drosophila S2 cells Histone H3 ChIP-seq from Drosophila S2 cells after CTCF/CP190 or ISWI-specific RNAi treatment
    Data Types:
    • Text
  • 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. ChIP-seq using anti-Trf2 and anti-TBP antibodies in Drosophila embryos
    Data Types:
    • Text
  • 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
  • ChIP against Opbp followed by next generation sequencing of Drosophila melanogaster embryos. Samples were sequenced using Illumina HiSeq and include four biological replicates, with both mock and input controls.
    Data Types:
    • Text
  • 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. ELAV ChIP-Seq assays were conducted with nuclei obtained from 6-8 hr and 10-12 hr embryos
    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
  • 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. 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.
    Data Types:
    • Text
  • The goal of this experiment was to identify genomic dCAP-D3 binding sites in Drosophila S2R+ cells 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.
    Data Types:
    • Text
    • File Set
  • 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
1