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  • dLint1 (CG1908) was ChIPseq`d in Drosophila melanogaster KC cells and S2 cells
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  • Accession Number: GSE83435 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) GPL22022: Illumina HiSeq 2500 (Drosophila miranda) Organism: Drosophila melanogaster Published on 2016-07-17 Summary: ChIP-seq was performed to compare binding the genome-wide binding profile of the CLAMP transcription factor in two different Drosophila species. Overall Design: ChIP seq experiments compare the binding profile of CLAMP in female larvae to identify conservation of its binding sequence. Contact: Name: Michael Tolstorukov Organization: Massachusetts General Hospital Deparment: Molecular Biology Address: 185 Cambridge Street Boston MA 02114 USA Email: tolstorukov@molbio.mgh.harvard.edu Organization: GEO Address: USA
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  • Accession Number: GSE52240 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-04-18 Summary: ChIP-Seq peak calling of CP190 in wild-type and Ibf2 mutant Drosophila melanogaster third instar larvae Overall Design: Two wild-type and two Ibf2 mutant Drosophila melanogaster third instar larvae were sequenced. Contact: Name: M Lluisa Espinas Organization: IBMB-CSIC Address: Baldiri Reixac 10 Barcelona 08028 Spain Email: mlebmc@ibmb.csic.es Organization: GEO Address: USA
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  • Accession Number: GSE15292 Platform: GPL6949: Agilent-019182 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 1 of 3 GPL6950: Agilent-019183 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 2 of 3 GPL6951: Agilent-019184 Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray 3 of 3 GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2009-03-20 Summary: 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. 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: 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. 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 peak calling of CP190 in wild-type and Ibf2 mutant Drosophila melanogaster third instar larvae Two wild-type and two Ibf2 mutant Drosophila melanogaster third instar larvae were sequenced.
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  • Accession Number: GSE49480 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) GPL10639: NimbleGen Drosophila melanogaster Whole Genome 2.1M tiling array GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2014-10-30 Summary: This SuperSeries is composed of the SubSeries listed below. Overall Design: Refer to individual Series Contact: Name: Brian Oliver Organization: NIDDK, NIH Laboratory: Developmental Genomics Deparment: LCDB Address: 50 South Drive Bethesda MD 20892 USA Email: briano@helix.nih.gov Phone: 301-496-5495 Organization: GEO Address: USA
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  • Accession Number: GSE36374 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) GPL15334: Illumina HiSeq 1000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-03-29 Summary: ChIP-seq was performed using Drosophila Kc167 cells using antibodies against H3K4me3 to identify active promoters and H3K4me1 to identify active enhancers. H3K27ac ChIPseq was performed to identify active promoters and enhancers. Once enhancers and promoters were identified, JIL-1 and histone phosphorylation, H3K9acS10ph and H3K27acS28ph, ChIP-seq was performed to look at binding trends. JIL-1 and phosphoacetlation is found at low levels at inactive enhancers and shows increase at active enhancers and promoters. Overall Design: Here we examine histone phosphorylation by JIL-1 and acetylation of H3K27ac by CBP at transcriptionally active vs. inactive promoters and enhancers. ChIP-seq is performed in Kc167 Drosophila cells using antibodies against JIL-1, H3K27acS28ph, H3K9acS10ph, H3K4me3, H3K4me1, and H3K27ac. 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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  • 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. ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila larvae
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  • Accession Number: GSE49102 Platform: GPL11203: Illumina Genome Analyzer IIx (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-05-01 Summary: 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 Overall Design: ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells 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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  • 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 Examination of CTCF binding in 4 Drosophila species and their correlation with gene expression levels in the same development stages
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