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  • 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
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  • 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
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  • 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.
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  • ChIP-chip and ChIP-seq data analysis workflow. ChIP-chip data (fold enrichment of immunoprecipitated material over genomic DNA) and/or ChIP-seq data are mapped to a reference genome. Control bound and unbound regions are visually inspected and validated by comparison to standard ChIP and qPCR. Genomic regions where signal is significantly greater than expected by chance (user-defined threshold) are identified as ‘bound’. Bound regions are then compared to a database of genomic elements of interest (e.g. promoters) to identify bound elements. Note that absence of detected binding from a genomic region may result from absence of complementary probes upon the array (ChIP-chip), masking of repetitive regions (ChIP-chip and ChIP-seq), or unmappable regions (ChIP-seq). ... Pol II distribution detected by ChIP, ChIP-chip, and ChIP-seq. Drosophila S2 cells were crosslinked, sonicated, and total Pol II (Rpb3) was immunoprecipitated. Pol II ChIP signal at the Tl promoter region was quantified with qPCR using primer pairs spaced on average every 100bp (blue line), ChIP-chip using Agilent Drosophila Whole Genome 2-ChIP sets with average probe spacing of 250bp (red line), or ChIP-seq reads sequenced with the Illumina Genome Analyzer (green line), binned in 25 nucleotide windows. Genomic positions are reported as bp×10−2, and represent the center point of primer pairs used, probe sequence, or window. ... ChIP-seq... Comparison of Pol II distribution as determined by ChIP-chip and ChIP-seq. The distribution of Pol II (Rpb3)-binding at the: (A) lace; (B) kay; (C) smi35A and; (D) CG6860/CLIP-190 genes was determined by ChIP-chip (NimbleGen HD2 Drosophila whole genome arrays) or ChIP-seq (Illumina Genome Analyzer reads binned in 25 nucleotide windows). ... Workflow for ChIP-chip and ChIP-seq experiments. Following experimental manipulation (yellow boxes), cells are crosslinked with formaldehyde, sonicated to fragment chromatin, and protein–DNA complexes immunoprecipitated with antibodies targeting the protein or modification of interest (here, Pol II). Following quality control qPCR to confirm expected ChIP signal at control regions, immunoprecipitated DNA is processed specifically for either ChIP-chip or ChIP-seq. ChIP-chip can provide information about all immunoprecipitated DNA sequences complementary to tiling array probes in a strand-insensitive manner. ChIP-seq provides information about all mappable sequences located at the 5′-ends of immunoprecipitated DNA (red and blue boxes). ... Pol II binding detected with differing ChIP-chip methods and platforms. Pol II (Rpb3) ChIP was performed with material generated from Drosophila S2 cells and binding was detected with NimbleGen HD2 Drosophila whole genome arrays or Agilent Drosophila Whole Genome 2-ChIP sets. Pol II-bound genomic regions were determined for the NimbleGen array with NimbleScan software (FDRDrosophila Release 5 Genomic sequence. Pol II-bound genomic regions were determined for the Agilent arrays with the Drosophila Release 3 Genomic sequence as previously described [4,5,48].
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  • 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
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  • 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
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  • 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
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  • ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin extracted from 2.5-6h w[1118] embryos and 6.5-12h w[1118] embryos. Samples from two time points were analyzed: 2.5-6h embryos and 6.5-12h embryos. In each time point there is one Insv ChIP sample and one IgG control sample.
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  • Accession Number: GSE44176 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-04-04 Summary: ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin extracted from 2.5-6h w[1118] embryos and 6.5-12h w[1118] embryos. Overall Design: Samples from two time points were analyzed: 2.5-6h embryos and 6.5-12h embryos. In each time point there is one Insv ChIP sample and one IgG control sample. Contact: Name: Jakub Orzechowski Westholm Organization: Memorial Sloan-Kettering Cancer Center Laboratory: Eric Lai Deparment: Developmental Biology Address: 1275 York Avenue, Box 252 New York NY 10065 USA Email: orzechoj@mskcc.org Organization: GEO Address: USA
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  • Accession Number: GSE84502 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-07-18 Summary: We developed a strategy to map GlcNAc modified proteins based on a chemical chromatin precipitation strategy. Drosophila S2 cells, as well as wild type (wt) and sxc null pupae, were fed with 100 uM Ac4GalNAz and the resulting DNA was cross-linked, sonicated, and purified. DNA strands cross-linked to GlcNAz proteins were isolated by congugating with alkyn-biotin by Staudinger ligation followed by streptavidin purification. The resulting DNA was constructed into libraries for sequencing. To asses the robustness of our strategy, we compared GalNAz ChIP-seq results in S2 cells with two other GlcNAc ChIP-seq strategies, using a mutant β-1,4-galactosyltransferase (GalT) and the lecting wheat germ agglutinin (WGA). Briefly, GalT was incubated with cross-linked, sonicated and purified DNA along with UDP-GalNAz. Ligation to biotin with click chemistry followed by streptavidin purification resulted in library ready material. For WGA and Pho ChIP-seq, cross-linked and purified DNA was incubated with pho antibody or WGA resin and purified followed by library preperation. Overall Design: Examination GlcNAc bound loci in Drosophila cells and pupae. Contact: Name: David Vocadlo Organization: Simon Fraser University Deparment: Chemistry Address: 8888 University Drive Burnaby British Columbia Canada Email: dvocadlo@sfu.ca Organization: GEO Address: USA
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