Contributors: Friederike Dündar, Thomas Conrad, Sarantis Chlamydas, Sunil J Raja, Fidel Ramirez, Filipe T Cadete, Asifa Akhtar

Date: 2016-04-25

Drosophila melanogaster) GPL13313: Illumina HiSeq 2000 (Drosophila virilis...Drosophila melanogaster) GPL9061: Illumina Genome Analyzer II (Drosophila...Drosophila melanogaster and Drosophila virilis Overall Design: ChIP-seq...Drosophila melanogaster Published on 2016-04-25 Summary: We report the...Drosophila melanogaster and Drosophila virilis Overall Design: ChIP-seq ... 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

Contributors: Jakub Orzechowski Westholm, Jakub Westholm, Qi Dai, Eric Lai

Date: 2013-04-04

ChIP-seq for Drosophila Insensitive, together with IgG control. Chromatin...Drosophila Insensitive, together with IgG control. Chromatin extracted...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... 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

Contributors: Ni X, Zhang YE, N�gre N, Chen S, Long M, White KP

Date: 2012-11-08

Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila...Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding...Drosophila pseudoobscura at white pre pupa stage; Second, triplicate RNA-seq...Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila...Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding...Drosophila pseudoobscura at white pre pupa stage; Second, triplicate RNA-seq...Drosophila species and their correlation with gene expression levels in...Drosophila white prepupa on Illumina Genome Analyzer ... 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

Contributors: Kevin P. White, Matthew Slattery

Date: 2010-08-11

Drosophila simulans) GPL9395: Illumina Genome Analyzer (Drosophila pseudoobscura...Drosophila yakuba) Organism: Drosophila melanogaster Published on 2010...Drosophila Tiling 2.0R Array GPL9058: Illumina Genome Analyzer (Drosophila ... 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

Contributors: Kramer JM, Kochinke K, Oortveld MA, Marks H, Kramer D, de Jong EK, Asztalos Z, Westwood JT, Stunnenberg HG, Sokolowski MB

Date: 2011-01-05

Drosophila larvae, as well as in Drosophila larvae for which the euchromatic...Drosophila larvae...ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila ... 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

Contributors: Yang J, Ramos E, Corces VG

Date: 2012-08-03

Drosophila species. DNA sample from ChIP for BEAF and input are collected...Drosophila speies but also limited to Drosophila spcies. BEAF associates...Drosophila species reveals BEAF association with gene pairs, and the results...Drosophila species...Drosophila spcies ... 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. DNA sample from ChIP for BEAF and input are collected for each of four Drosophila species

Contributors: M Lluisa Espinas, Maria L Espinàs, Sergi Cuartero

Date: 2014-04-18

ChIP-Seq peak calling of CP190 in wild-type and Ibf2 mutant Drosophila...Drosophila melanogaster third instar larvae Overall Design: Two wild-type...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila melanogaster third instar larvae were sequenced. Contact: ... 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

Contributors: unknown

Date: 2015-05-01

Drosophila melanogaster S2 cells...ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample...Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes ... 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 ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample in Drosophila melanogaster S2 cells

Contributors: Kevin White, R K Arthur, K P White

Date: 2013-08-17

Drosophila species: Drosophila melanogaster, Drosophila simulans, Drosophila...Drosophila pseudoobscura) GPL11000: Illumina Genome Analyzer (Drosophila...Drosophila melanogaster Published on 2013-08-17 Summary: This data consists...Drosophila melanogaster) GPL9394: Illumina Genome Analyzer (Drosophila...ChIP-seq data can be found in GSE27111 [for melanogaster], GSE23537 SuperSeries...Drosophila species and its correlation with gene expression levels in ...Drosophila white prepupa on Illumina Genome Analyzer ... 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

Contributors: Helen McNeill, Kelvin Yeung

Date: 2017-03-16

ChIP-seq against endogenous Atro. These data sets will serve as a valuable...ChIP-seq and was used as a control. Contact: Name: Helen McNeill Organization...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila S2 cells...ChIP-seq experiments in untreated S2 cells. A corresponding non-specific...Drosophila Atro mutants have a large range of phenotypes, including neurodegeneration ... 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