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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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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. 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).
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This SuperSeries is composed of the following subset Series: GSE26895: Drosophila LID RNAi gene expression profiling GSE27078: LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster GSE40599: POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster Refer to individual Series
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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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dLint1 (CG1908) was ChIPseq`d in Drosophila melanogaster KC cells and S2 cells
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This data consists of RNA-seq data of whole animal white pre pupa of four Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila yakuba, and Drosophila pseudoobscura. The processed RPKM values are calculated following the method in Garber et al 2011 Nature Methods paper. Examination of H3K27me3 in 4 Drosophila species and its correlation with gene expression levels in the same development stage relevant ChIP-seq data can be found in GSE25663, GSE25668
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ChIP-Seq peak calling of CP190 in wild-type and Ibf2 mutant Drosophila melanogaster third instar larvae Two wild-type and two Ibf2 mutant Drosophila melanogaster third instar larvae were sequenced.
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ChIP-seq study analysing adult Drosophila melanogaster head, glial, neuronal and fat body, as well as embryonic RNA pol II and H2A.v binding by employing the GAL4-UAS system to generate GFP-fusion proteins and ChIP-seq
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The Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes binding of the euchromatic dHP1c/WOC/ROW-complex (dHP1EU) to the transcription-start site (TSS) of active genes ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells
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ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation ChIP-seq experiments compared the binding profiles of CLAMP in male and female cells and mRNA-seq data to define the role of CLAMP in regulating genes on the X-chromosome
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