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  • Accession Number: GSE84502 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-07-18 Summary: We developed a strategy to map GlcNAc modified proteins based on a chemical chromatin precipitation strategy. Drosophila S2 cells, as well as wild type (wt) and sxc null pupae, were fed with 100 uM Ac4GalNAz and the resulting DNA was cross-linked, sonicated, and purified. DNA strands cross-linked to GlcNAz proteins were isolated by congugating with alkyn-biotin by Staudinger ligation followed by streptavidin purification. The resulting DNA was constructed into libraries for sequencing. To asses the robustness of our strategy, we compared GalNAz ChIP-seq results in S2 cells with two other GlcNAc ChIP-seq strategies, using a mutant β-1,4-galactosyltransferase (GalT) and the lecting wheat germ agglutinin (WGA). Briefly, GalT was incubated with cross-linked, sonicated and purified DNA along with UDP-GalNAz. Ligation to biotin with click chemistry followed by streptavidin purification resulted in library ready material. For WGA and Pho ChIP-seq, cross-linked and purified DNA was incubated with pho antibody or WGA resin and purified followed by library preperation. Overall Design: Examination GlcNAc bound loci in Drosophila cells and pupae. Contact: Name: David Vocadlo Organization: Simon Fraser University Deparment: Chemistry Address: 8888 University Drive Burnaby British Columbia Canada Email: dvocadlo@sfu.ca Organization: GEO Address: USA
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  • Accession Number: GSE85404 Platform: GPL19951: Illumina HiSeq 1500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2018-01-01 Summary: The nature of chromatin as regular succession of nucleosomes has gained iconic status. The average nucleosome repeat length (NRL) determined by classical means serves as index for bulk chromatin of a given specimen. However, this value is dominated by regular heterochromatin since nucleosomal arrays are often not regular at individual single copy sequences. To obtain a measure for nucleosome regularity in euchromatin we subjected nucleosome dyad profiles to autocorrelation and spectral density analyses. This revealed variation in nucleosome regularity and NRL at different types of euchromatin and yielded a comprehensive catalog of regular phased nucleosome arrays (PNA). The absence of the nucleosome sliding factor ACF1 correlated with global loss of regularity in euchromatin and increased NRL and compromised phasing at a novel type of PNA. Our approach is generally applicable to characterize hallmarks of euchromatin organization. Overall Design: ChIP-Seq in Drosophila melanogaster embryos Contact: Name: Tobias Straub Organization: LMU Munich Deparment: Biomedical Center, Bioinformatics Address: Großhadener Str. 9 Martinsried 82152 Germany Email: tstraub@med.uni-muenchen.de Organization: GEO Address: USA
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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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  • Accession Number: GSE44176 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-04-04 Summary: ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin extracted from 2.5-6h w[1118] embryos and 6.5-12h w[1118] embryos. Overall Design: Samples from two time points were analyzed: 2.5-6h embryos and 6.5-12h embryos. In each time point there is one Insv ChIP sample and one IgG control sample. Contact: Name: Jakub Orzechowski Westholm Organization: Memorial Sloan-Kettering Cancer Center Laboratory: Eric Lai Deparment: Developmental Biology Address: 1275 York Avenue, Box 252 New York NY 10065 USA Email: orzechoj@mskcc.org Organization: GEO Address: USA
    Data Types:
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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 ChIP-chip data on Agilent 244K dual-color arrays for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. This SuperSeries is composed of the following subset Series: GSE15422: ChIP-chip of H3K9me3 in Drosophila at different time points of development GSE15423: ChIP-chip of H3K27me3 in Drosophila at different time points of development GSE15424: ChIP-chip of H3K4me3 in Drosophila at different time points of development GSE15425: ChIP-chip of H3K4me1 in Drosophila at different time points of development GSE15426: ChIP-chip of H3K9Ac in Drosophila at different time points of development GSE15427: ChIP-chip of CBP/p300 in Drosophila at different time points of development GSE15430: ChIP-chip of H3K27Ac in Drosophila at different time points of development GSE16013: Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq GSE16702: ChIP-chip of PolII in Drosophila at different time points of development GSE18068: Genome-wide maps of chromatin state in staged Drosophila embryos, RNA-seq For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf ChIP-chip: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays. ChIP-seq: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure. RNA-seq: For each time-point (E-0-4h, E-4-8h, E-8-12h, E-12-16h, E-16-20h, E20-24h, L1, L2, L3, Pupae, Adult Males and Adult Females) a total RNA extraction has been performed. After conversion into double stranded DNA, the samples have been sequenced in duplicate on Solexa Genome Analyzer following Solexa sequencing procedure.
    Data Types:
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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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    • Sequencing Data
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  • Accession Number: GSE61340 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) GPL13313: Illumina HiSeq 2000 (Drosophila virilis) Organism: Drosophila melanogaster Published on 2016-04-25 Summary: We report the binding of MSL1 protein in male, female and mof2 mutant samples of Drosophila melanogaster and Drosophila virilis Overall Design: ChIP-seq of MSL1 in male and female fly samples Contact: Name: Friederike Dündar Organization: Weill Cornell Medicine Laboratory: Applied Bioinformatics Core Deparment: Physiology & Biophysics Address: 1300 York Ave New York New York 10065 USA Email: frd2007@med.cornell.edu Organization: GEO Address: USA
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  • CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. We have generated CBP ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data. This shows that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb Response Elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. ChIP seq in Drosophila S2 cells using two different antibodies against CBP (nejire), one raised in rabbit against amino acids 2540-3190 (CBP rb), and one raised in guinea-pig against amino acids 1-178 (CBP gp)
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  • Accession Number: GSE100613 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-10-20 Summary: TFIIB chromatin binding is drastically reduced genome-wide after 10 min of CBP (also known as nejire) inhibition. Overall Design: Drosophila melanogaster S2 cells were treated with control (C37) or the CBP inhibitor C646 for 10 min, fixed with with formaldehyde, and chromatin prepared. One percent Drosophila virilis chromatin was mixed with this chromatin (spike-in). An antibody raised against Drosophila TFIIB (gift from Jim Kadonaga, UCSD) was used for ChIP-seq. Contact: Name: Mattias Mannervik Organization: Stockholm University Laboratory: Mattias Mannervik Deparment: Molecular Biosciences, the Wenner-Gren Institute Address: Arrheniuslaboratories E3 Stockholm 10691 Sweden Email: mattias.mannervik@su.se Organization: GEO Address: USA
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  • Accession Number: GSE23537 Platform: GPL6629: [DM_tiling2_MR] Affymetrix Drosophila Tiling 2.0R Array 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 2010-08-11 Summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series 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: Affymetrix, Inc. Address: Santa Clara CA 95051 USA Email: geo@ncbi.nlm.nih.gov, support@affymetrix.com Phone: 888-362-2447 Web-Link: http://www.affymetrix.com/index.affx
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