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  • Accession Number: GSE84595 Platform: GPL14601: AB SOLiD 4 System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2016-11-22 Summary: ChIP-seq Y14 Overall Design: Y14 ChIP-seq in S2 cells Contact: Name: Saverio Brogna Organization: University Birmingham Address: Edgbaston Birmingham United Kingdom Email: s.brogna@bham.ac.uk Organization: GEO Address: USA
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  • Accession Number: GSE42086 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-11-15 Summary: ChIP-seq was performed using Drosophila Kc167 cells using antibodies against the two isoforms of Fs(1)h, the Brd4 homologue. Differences in binding patterns between the two isoforms are described. Overall Design: We examined the differences in Fs(1)h isoform binding across the genome and describe the short isoform to be correlated with transcription at enhancers and promoters. The long isoform is found predominately at insulator binding sites where multiple insulators are bound. Contact: Name: Wendy A Kellner Organization: Emory University Laboratory: Victor Corces Deparment: Biology Address: 1510 Clifton Road Atlanta GA 30322 USA Email: wkellne@emory.edu Phone: 404-727-4250 Organization: GEO Address: USA
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  • Accession Number: GSE35648 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) GPL9958: Illumina Genome Analyzer II (Drosophila pseudoobscura) GPL13305: Illumina Genome Analyzer II (Drosophila simulans) GPL13312: Illumina Genome Analyzer II (Drosophila virilis) Organism: Drosophila melanogaster Published on 2012-08-03 Summary: Insulators are considered as chromosome organizers. BEAF, one of the insulator proteins, is highly conserved in Drosophila speies but also limited to Drosophila spcies. BEAF associates with TSS of active genes. Comparative study of BEAF binding landscapes in four Drosophila species reveals BEAF association with gene pairs, and the results suggest the role of gain or loss of BEAF binding during the speciation of Drosophila species. Overall Design: DNA sample from ChIP for BEAF and input are collected for each of four Drosophila species Contact: Name: Jingping Yang Organization: Emory Address: 1507 Clifton Rd Atlanta GA 30322 USA Email: idayang@hotmail.com Organization: GEO Address: USA
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  • Accession Number: GSE97127 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-03-30 Summary: To investigate the mechanisms of gene regulation during Drosophila spermatogenesis, we studied the effects of comr and can mutations on the chromatin of the cells in Drosophila testes by H3K27me3 ChIP-Seq. Overall Design: ChIP-Seq of H3K27me3 histone modification in comr- and can-mutant testes of Drosophila melanogaster. We processed two biological replicates of every sample and corresponding input specimen. Contact: Name: Petr Laktionov Organization: Institute of molecular and cellular biology SD RAS Laboratory: Genomics lab Address: Lavrenitev ave 8/2 Novosibirsk Russia Email: laktionov@mcb.nsc.ru Organization: GEO Address: USA
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  • Accession Number: GSE56550 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-07-23 Summary: We have analyzed ChIP-Seq of H3K9ac and H3K27me3 in wing imaginal discs and eye imaginal discs from Drosophila melanogaster. Overall Design: Examination of two histone modifications in wing/eye imaginal discs cells Contact: Name: Enrique Blanco Organization: Center for Genomic Regulation (CRG) Laboratory: Epigenetic Events in Cancer (L. Di Croce's lab) Deparment: Gene Regulation, Stem Cells and Cancer Address: Dr. Aiguader 88 Barcelona 08003 Spain Email: enrique.blanco@crg.eu Phone: +34 93 316 01 00 Organization: GEO Address: USA
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  • Accession Number: GSE19325 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-04-16 Summary: We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. In order to address the possibility that distinct techniques are responsible for such a difference, we also use the Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results directly with published work using ChIP-chip and microarray on S2 cells. For the S2 cell ChIP-chip data, we used data from the following paper: Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K: RNA polymerase is poised for activation across the genome. /Nat Genet /2007, 39(12):1507-1511. The accession number for this data is: GSE6714. Overall Design: ChIP-seq: Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 cells Profiling chromatin structure in bam testis using antibodies against 3 histone modifications and RNA Pol II RNA-seq: Profiling transcriptome of S2 cells using RNA-seq Contact: Name: Dustin E Schones Organization: City of Hope Deparment: Cancer Biology Address: 1500 E Duarte Rd. Duarte CA 91010 USA Email: dschones@coh.org Organization: GEO Address: USA
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  • Accession Number: GSE63494 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2016-12-01 Summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context. Overall Design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment. Contact: Name: Barbara M Bryant Organization: Constellation Pharmaceuticals Address: 215 First Street Cambridge MA 02142 USA Email: barbara.bryant@constellationpharma.com Phone: 617-714-0561 Organization: GEO Address: USA
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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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  • Accession Number: GSE64243 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2016-01-31 Summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context. Overall Design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment. Contact: Name: Suchit Jhunjhunwala Organization: Genentech Address: 1 DNA Way, MS-93 South San Francisco CA 94080 USA Email: suchitj@gene.com Organization: GEO Address: USA
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  • ChiP-seq profiling of Drosophila melanogaster salivary glands to identify targets for NSL1 and MCRS2.
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