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  • Accession Number: GSE22447 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2011-01-05 Summary: This study describes the epigenetic profiling of the H3K9me2 in wt Drosophila larvae, as well as in Drosophila larvae for which the euchromatic catalytic enzyme depositing H3K9me2 (EHMT) is knocked out. Overall Design: ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila larvae Contact: Name: Hendrik Marks Organization: NCMLS Radboud University Nijmegen Deparment: Molecular Biology Address: Geert Grooteplein 26/28 Nijmegen Netherlands Email: h.marks@ncmls.ru.nl Organization: GEO Address: USA
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  • Accession Number: GSE49945 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL9394: Illumina Genome Analyzer (Drosophila simulans) GPL9395: Illumina Genome Analyzer (Drosophila pseudoobscura) GPL11000: Illumina Genome Analyzer (Drosophila yakuba) Organism: Drosophila melanogaster Published on 2013-08-17 Summary: 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. Overall Design: 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 GSE27111 [for melanogaster], GSE23537 SuperSeries [for simulans, yakuba, and pseudoobscura] (SubSeries: GSE25663, GSE25668, GSE50819) Contact: Name: Kevin White Organization: University of Chicago Laboratory: Kevin White lab Deparment: Institute for Genomics and Systems Biology Address: 900 E. 57th St. Room 10100 Chicago IL 60637 USA Organization: GEO Address: USA
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  • Accession Number: GSE49842 Platform: GPL9521: AB SOLiD System 2.0 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-08-13 Summary: The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells Overall Design: Polyclonal antibody raised against M1BP was used to immunoprecipitate M1BP-DNA adducts generated by treating Drosophila cells with formaldehyde, lysing the cells, and shearing DNA by sonication. Immunoprecipitated DNA was sequenced using the AB SOLiD system. Contact: Name: David Scott Gilmour Organization: Penn State University Laboratory: Gilmour Deparment: Biochemistry and Molecular Biology Address: 465 North Frear University Park Pennsylvania 16802 USA Email: dsg11@psu.edu Phone: 814-863-8905 Organization: GEO Address: USA
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  • Accession Number: GSE87509 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-03-16 Summary: Drosophila Atro mutants have a large range of phenotypes, including neurodegeneration, segmentation, patterning and planar polarity defects. Although Atro mutants have diverse phenotypes, little is known about Atro’s binding partners and downstream targets. We present the first genomic analysis of Atro using ChIP-seq against endogenous Atro. These data sets will serve as a valuable resource for future studies on Atro. Overall Design: We performed three independent biological replicates of Atro ChIP-seq experiments in untreated S2 cells. A corresponding non-specific IgG control ChIP was performed with each Atro ChIP-seq and was used as a control. Contact: Name: Helen McNeill Organization: Lunenfeld Tanenbaum Research Institute Address: 600 University Ave. Toronto Ontario Canada Email: mcneill@lunenfeld.ca Organization: GEO Address: USA
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  • Accession Number: GSE89459 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-08-25 Summary: trr ChIP-seq, trr RNA-seq, G9a RNA-seq Overall Design: trr ChIP-seq profiles on 0-5 day old fly heads in two replicates and mRNA profiles of trr- and G9a mutant 0-5 days old fly heads in two and three replicates respectively. Contact: Name: Tom Koemans Organization: Radboudumc Laboratory: van Bokhoven/ Schenck Deparment: Human genetics Address: Geert Grooteplein 10 Nijmegen Netherlands Email: tom.koemans@radboudumc.nl Organization: GEO Address: USA
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  • Accession Number: GSE38558 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-06-07 Summary: modENCODE_submission_4351 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We will precisely identify sequence elements that direct DNA replication by using chromatin immunoprecipitation of known replication initiation complexes. These experiments will be conducted in multiple cell types and developmental tissues. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic disc; Developmental Stage: third instar larval stage; Sex: Male; EXPERIMENTAL FACTORS: Strain ; Antibody dORC2 (target is Drosophila ORC2p); read length (read_length) Contact: Name: DCC modENCODE Organization: Ontario Institute for Cancer Research Laboratory: modENCODE DCC Address: MaRS Centre, South Tower, 101 College Street, Suite 800 Toronto Ontario Canada Email: help@modencode.org Phone: 416-673-8579 Organization: GEO Address: USA
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  • Accession Number: GSE24449 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL9394: Illumina Genome Analyzer (Drosophila simulans) GPL9395: Illumina Genome Analyzer (Drosophila pseudoobscura) GPL11000: Illumina Genome Analyzer (Drosophila yakuba) Organism: Drosophila melanogaster Published on 2012-11-08 Summary: This is a dataset which comprises the following two different kinds of genomic data in Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding factor) binding profiles in each of the four closely related Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila yakuba and Drosophila pseudoobscura at white pre pupa stage; Second, triplicate RNA-seq data of white pre pupa whole animals of three Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila yakub. The binding site/region/peaks are called using a modified method of QuEST( please see details in our related publication). The sequence read counts and RPKM values are calculated following the method in Mortazavi et al 2008 Nature Methods paper. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall Design: Examination of CTCF binding in 4 Drosophila species and their correlation with gene expression levels in the same development stages Contact: Name: Kevin P. White Organization: University of Chicago Deparment: Institute for Genomics and Systems Biology Address: 900 E. 57th STR. 10th FL. Chicago IL 60615 USA Email: kpwhite@uchicago.edu Organization: GEO Address: USA
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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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  • Accession Number: GSE39271 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-07-15 Summary: ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation Overall Design: 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 Contact: Name: Erica Larschan Organization: Brown University Address: 185 Meeting St. Providence 02912 USA Email: Erica_Larschan@brown.edu Organization: GEO Address: USA
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  • Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs
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