Filter Results
1194 results
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
    • File Set
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
    • File Set
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
  • 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
    Data Types:
    • Text
5