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This SuperSeries is composed of the following subset Series: GSE29517: ChIP-chip from Drosophila egg chambers using ORC2 antibody GSE29518: ChIP-chip from dissected Drosophila egg chambers using antibody recognizing RNAPII GSE29520: ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4 GSE29526: Expression profile of 16C ovarian follicle cells Refer to individual Series
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We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development. 2 biological replicates of ChIP-seq with anti-So antibody on chromatin from D. melanogaster third instar eye-antennal imaginal discs; negative control - same sample and ChIP-seq protocol without anti-So antibody
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JAK/STAT pathway plays important roles in controlling Drosophila intestinal homeostasis and regulating the ISC proliferation and differentiation. However,the downstream targets of its transcription factor-STAT92E remain largely unknown.To further identify the regualtory mechanisms of the JAK/STAT pathway in controlling intestinal homeostasis,we performed the ChIP-Seq assay with mouse raised STAT92E antibody using JAK/STAT signaling highly activated adult intestines.Through the ChIP assay, we have identified over 1000 significant peaks (p<0.01) around the putative targets.The well-characterized JAK/STAT downstream targets including Domeless,Socs36E,STAT92E and chinmo were identified in our ChIP assay,indicating that our experiment is workable to identify novel JAK/STAT downstream targets in adult intestines.This work will provide insights into our understanding of regulatory mechanisms of JAK/STAT signaling during Drosophila intestinal development. Identify the ChIP peaks of STAT92E antibody using JAK/STAT signaling highly actived Drosophila adult intestines, compared with input libaray as the control
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Subcellular localization and genomic binding of BmCdp1 in BmN4 cells. (A) Western blotting. Flag-tagged BmCdp1 was detected using anti-Flag antibody. Actin was used as a control. N and C indicate nuclear and cytoplasmic fractions, respectively. (B) Immunohistostaining. BmN4 cells were probed with anti-Flag antibody, and visualized using Alexa Fluor 546-conjugated goat anti-mouse IgG. The cells were also counterstained with DAPI to visualize nuclear DNA. (C) ChIP-seq. Mapping patterns of ChIP-seq data from pIZ- and Flag-tagged BmCdp1-transfected cells were visualized using Genome studio (Illumina). A representative BmCdp1-enriched locus on chromosome 17 is shown. The primer sets used in Fig. 3D are indicated. (D) ChIP-qPCR. BmCdp1 enrichment on chromosome 17 was verified by ChIP-qPCR. ... ChIP-seq and ChIP-qPCR of BmCdp1-enriched locus on chromosome 10. (A) ChIP-seq. Mapping patterns, generated using ChIP-seq data, from pIZ- and Flag-tagged BmCdp1-transfected cells were visualized using Genome studio (Illumina). A representative BmCdp1-enriched locus on chromosome 10 is shown. The primer sets used in Fig. S2A were indicated. (B) ChIP-qPCR. BmCdp1 enrichment on chromosome 10 was verified by ChIP-qPCR. ... In this study, we discovered a novel gene with two CDs in the Bombyx genome. This gene, BmCdp1, encodes a nuclear protein that can bind to specific loci in the Bombyx genome. Phylogenetic analysis revealed that the Drosophila orthologs of BmCdp1 were CG8289 genes (Fig. 1C), but D. melanogaster CG8289 lacked one of the two CDs that were present in BmCdp1 (Fig. S1). In FlyBase, seven alleles have been found in D. melanogaster at this locus, three of which (CG8289d10824, CG8289GD13880, and CG8289GD16515) have been listed as viable and one (CG8289d1082) has been categorized as fertile. Similar to our observation in Bombyx (Fig. 2C), peak expression of CG8289 was observed within the 6–12hour embryonic stages. In addition, the FlyAtlas Anatomical Expression Data demonstrated that almost all larval and adult tissues express CG8289 at moderate levels, suggesting that Cdp1 expression profiles are conserved between these two insects. In the present study, no phenotypic abnormalities were observed in BmCdp1-knocked down embryos, suggesting that BmCdp1 is probably dispensable for silkworm embryogenesis. Further experiments, such as gene knockout studies using TALENs (Ma et al., 2012; Sajwan et al., 2013), will be necessary to understand the role of this gene at other developmental stages.... Domain structure of BmCdp1 orthologs in Drosophila species. BmCdp1 orthologs of Drosophila melanogaster and Drosophila persimilis have a single CD, whereas the others possess two CDs. ... Because BmCdp1 is a nuclear protein, it potentially interacts with modified histones via its CDs. To test this hypothesis, we investigated the BmCdp1-enriched genomic loci by ChIP-seq. We have recently constructed an epigenome map of BmN4 cell line (Kawaoka et al., 2013), allowing us to get information on gene expression and histone modifications at the interest genomic loci easily. Therefore, we used this cell line in ChIP-seq studies. We performed ChIP-seq analysis of control (pIZ vector-transfected) and Flag-tagged BmCdp1-transfected cells with anti-Flag antibody. First, we attempted to visually identify the BmCdp1-enriched loci using Genome studio, and detected a few distinct peaks (<10) after comparing the data from control cells (Figs. 3C, S2A). Similar results were obtained using the MACS program (data not shown). Consequently, we verified the observed enrichment at 8 loci by ChIP-qPCR, and identified two genomic loci on chromosomes 10 and 17, where BmCdp1 was reliably enriched (Figs. 3D, S2B). According to the Bombyx genome database, one of the two loci was localized upstream region of a putative gene, BGIBMGA007060 (Fig. 3C), suggesting that BmCdp1 occupancy at this locus affected BGIBMGA007060 transcription.
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.yak_WPP generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Pcl-D2 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Psq-D2 from D.yak_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.pse_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.pse_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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