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  • Accession Number: GSE103291 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-12-13 Summary: This analysis largely reflected the genomic distribution of dBigH1 in 0-2hpf early embryos. In these studies, we observed that dBigH1 was uniformely distributed across the genome. Overall Design: ChIP-Seq peak calling of dBigH1 against input sample in early embryos Contact: Name: Oscar Reina Garcia Organization: IRB Barcelona Deparment: Biostatistics and Bioinformatics Address: C/Baldiri Reixac 10 Barcelona Barcelona 08028 Spain Email: oscar.reina@irbbarcelona.org Organization: GEO Address: USA
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  • Accession Number: GSE40664 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-02-06 Summary: Genome-wide mapping of protein–DNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIPseq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIPseq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIPseq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE). Overall Design: ChIP-seq for Twist transcription factor in Drosophila embryos Contact: Name: Samuel Richard Meier Organization: Stowers Institute for Medical Research Laboratory: Computational Biology Address: 1000 E 50th Street Kansas City MO 64110 USA Email: srm@stowers.org Phone: 816-926-4455 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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  • This SuperSeries is composed of the following subset Series: GSE37027: Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq] GSE37032: Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq] Refer to individual Series
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  • Accession Number: GSE51134 Platform: GPL15334: Illumina HiSeq 1000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-09-25 Summary: Transcription and pre-mRNA alternative splicing are highly regulated processes that play major roles in modulating eukaryotic gene expression. It is increasingly apparent that other pathways of RNA metabolism, including small RNA biogenesis, can regulate these processes. However, a direct link between alternative pre- mRNA splicing and small RNA pathways has remained elusive. Here we show that the small RNA pathway protein Argonaute-2 (Ago-2) regulates alternative pre-mRNA splicing patterns of specific transcripts in the Drosophila nucleus using genome-wide methods in conjunction with RNAi in cell culture and Ago-2 deletion or catalytic site mutations in Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to specific chromatin sites near gene promoters and negatively regulates the transcription of the Ago-2-associated target genes. These transcriptional target genes are also bound by Polycomb group (PcG) transcriptional repressor proteins and change during development, implying that Ago-2 may regulate Drosophila development. Impor- tantly, both of these activities were independent of the catalytic activity of Ago-2, suggesting new roles for Ago-2 in the nucleus. Finally, we determined the nuclear RNA-binding profile of Ago-2, found it bound to several splicing target transcripts, and identified a G-rich RNA-binding site for Ago-2 that was enriched in these transcripts. These results suggest two new nuclear roles for Ago-2: one in pre-mRNA splicing and one in transcriptional repression. Overall Design: Input chromatin, 2 replicates of Ago2 ChIP-seq Contact: Name: Matthew Taliaferro Organization: MIT Deparment: Biology Address: 77 Massachusetts Ave Cambridge MA 02144 USA Organization: GEO Address: USA
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  • Accession Number: GSE96959 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-12-13 Summary: This analysis largely reflected the genomic distribution of dBigH1 in spermatocytes since the vast majority of dBigH1-expressing cells in testes correspond to spermatocytes. In these studies, we observed that dBigH1 was not uniformely distributed across the genome. Overall Design: ChIP-Seq peak calling of dBigH1 against input sample in whole testes Contact: Name: Oscar Reina Garcia Organization: IRB Barcelona Deparment: Biostatistics and Bioinformatics Address: C/Baldiri Reixac 10 Barcelona Barcelona 08028 Spain Email: oscar.reina@irbbarcelona.org Organization: GEO Address: USA
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  • Mono-methylation of histone H3 on lysine 4 (H3K4me1) and acetylation of histone H3 on lysine 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and enhancers. Although in yeast all H3K4 methylation patterns including H3K4me1 are implemented by Set1/COMPASS, there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac in various tissues. Assays with the cut wing margin enhancer imply a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrates that Trr is required for H3K4me1 and H3K27ac on chromatin signatures that resemble the histone modification patterns described for enhancers. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 mono-methyltransferase Trr, and the H3K27 demethylase, UTX, cooperate to regulate the transition from inactive/poised to active enhancers. ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in WT and Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila S2 cells. ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1(-/-), MLL3(+/+), and MLL3(-/-) Mouse Embryonic Fibroblasts (MEFs).
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  • Accession Number: GSE55932 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-11-10 Summary: We analyzed gamma-H2Av ChIP-Seq from hand dissected salivary glands of wandering third instar larvae from wild-type (OrR) or suppressor of under-replication (SuUR) mutant Drosophila. Goals were to determine the DNA damage profile relative to underreplicated domains. We analyzed SUUR and Cdc45 ChIP-Seq from hand dissected early (stage 10) and late (stage 12/13) egg chambers from adult Drosophila ovaries. The goals was to determine the localization of SUUR relative to replication forks. Overall Design: ChIP-Seq of gamma-H2Av bound to third instar salivary gland DNA in WT and SuUR mutant Drosophila, analyzed by Illumina sequencing. One replicate is included for each of OrR (WT) or SuUR salivary glands.Rabbit IgG controls are included for OrR (WT). ChIP-Seq of SUUR and Cdc45 bound to egg chamber DNA from early and late stage egg chambers, analyzed by Illumina sequencing. One replicate is 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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  • Drosophila
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  • Accession Number: GSE38559 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-06-07 Summary: modENCODE_submission_4352 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: Antibody Anti-RNA polymerase II clone CTD4H8 (target is RNA polymerase II) 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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