Contributors: Kellner WA, Ramos E, Van Bortle K, Takenaka N, Corces VG

Date: 2012-03-29

ChIP-seq was performed to look at binding trends. JIL-1 and phosphoacetlation...ChIP-seq of Kc167 cells from Drosophila...ChIP-seq was performed using Drosophila Kc167 cells using antibodies against...ChIP-seq is performed in Kc167 Drosophila cells using antibodies against ... 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. 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.

Contributors: Brian Oliver, Sarah Bray

Date: 2014-10-30

Drosophila melanogaster) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster...Drosophila melanogaster Published on 2014-10-30 Summary: This SuperSeries...ChIP-seq, DamID-seq and DamID-chip and transcriptional response to DSX...Drosophila melanogaster) GPL10639: NimbleGen Drosophila melanogaster Whole ... 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

Contributors: Hendrik Marks, Jamie M Kramer, Korinna Kochinke, Merel A Oortveld, Daniela Kramer, Eiko K deJong, J T Westwood, Zoltan Asztalos, Hendrik G Stunnenberg, Marla B Sokolowski

Date: 2011-01-05

Drosophila larvae, as well as in Drosophila larvae for which the euchromatic...ChIP-Seq sequencing of H3K9me2 in third instar Drosophila larvae...ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE22447 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2011-01-05 Summary: 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. Overall Design: ChIP-Seq profiling of H3K9me2 in wt and EHMT KO third instar Drosophila larvae Contact: Name: Hendrik Marks Organization: NCMLS Radboud University Nijmegen Deparment: Molecular Biology Address: Geert Grooteplein 26/28 Nijmegen Netherlands Email: h.marks@ncmls.ru.nl Organization: GEO Address: USA

Contributors: Erica Larschan, Eric Bishop

Date: 2013-07-15

Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila dosage compensation...ChIP-seq experiments compared the binding profiles of CLAMP in male and...ChIP-seq and mRNA-seq experiments were performed to understand the role ... Accession Number: GSE39271 Platform: GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-07-15 Summary: ChIP-seq and mRNA-seq experiments were performed to understand the role of the CLAMP protein in dosage compensation Overall Design: ChIP-seq experiments compared the binding profiles of CLAMP in male and female cells and mRNA-seq data to define the role of CLAMP in regulating genes on the X-chromosome Contact: Name: Erica Larschan Organization: Brown University Address: 185 Meeting St. Providence 02912 USA Email: Erica_Larschan@brown.edu Organization: GEO Address: USA

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...ChIP-seq data of H3K27me3 and RNA-seq data in Drosophila white prepupa...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 ... 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: Kevin P. White, Kevin P White, Nicolas N Negre, Parantu K Shah

Date: 2009-03-20

Drosophila melanogaster Whole Genome ChIP-on-Chip Set 244K, Microarray...ChIP-seq: For each combination of time-point and antibody, triplicate ...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila at different time points of development: ChIP-chip, ChIP-seq ... 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

Contributors: Jingping Yang, Victor Corces

Date: 2012-08-03

Drosophila melanogaster Published on 2012-08-03 Summary: Insulators ...Drosophila simulans) GPL13312: Illumina Genome Analyzer II (Drosophila...Drosophila species. Overall Design: DNA sample from ChIP for BEAF and...ChIP-seq study of BEAF binding in four Drosophila spcies...Drosophila speies but also limited to Drosophila spcies. BEAF associates...Drosophila melanogaster) GPL9958: Illumina Genome Analyzer II (Drosophila ... 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

Contributors: Oscar Reina Garcia, Roman Kessler, Fernando Azorín

Date: 2015-05-01

Drosophila melanogaster) Organism: Drosophila melanogaster Published...ChIP-Seq]...ChIP-Seq peak calling of WOC, ROW, Z4, HP1c and Dsk2 against Input sample...Drosophila ubiquitin receptor dDsk2 associates to chromatin and stabilizes...Drosophila melanogaster S2 cells Contact: Name: Oscar Reina Garcia Organization ... 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

Contributors: Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S

Date: 2015-02-13

Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq...Drosophila eye primordium as a model system: FAIRE-seq, based on physical...ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs...Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq...Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq ... Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes. FAIRE-Seq in Drosophila wild type eye-antennal imaginal discs (2 wt strains); ATAC-Seq in Drosophila wild type eye-antennal imaginal discs (3 wt strains) ; FAIRE-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila Ras/Scrib induced eye disc tumors (1 early and 1 late); ATAC-Seq in Drosophila eye discs with Unpaired over-expression (2 biological replicates); CTCF ChIP-seq in Drosophila eye discs; ChIP-seq input in Drosophila eye discs

Contributors: Dustin E Schones, Qiang Gan, Dustin Schones, SukHo Eun, Gang Wei, Kairong Cui, Keji Zhao, Xin Chen

Date: 2010-04-16

ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures...Drosophila testis...Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results...ChIP-seq: Profiling chromatin modifications using antibodies against 3...Drosophila strain that allows us to obtain enough cells at their primitive...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE19325 Platform: GPL9061: Illumina Genome Analyzer II (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2010-04-16 Summary: We use male gonads isolated from a Drosophila strain that allows us to obtain enough cells at their primitive status as the starting material to study the endogenous chromatin structure of undifferentiated cells using ChIP-seq. We integrate the ChIP-seq data with RNA-seq data that measures the transcriptome in a digital manner. Our genome-wide analyses indicate that the majority of differentiation genes in undifferentiated cells lack an active chromatin mark and paused Pol II; instead, they are associated with either the repressive H3K27me3 mark or no detectable mark. In order to address the possibility that distinct techniques are responsible for such a difference, we also use the Drosophila S2 cells to perform ChIP-seq and RNA-seq and compare the results directly with published work using ChIP-chip and microarray on S2 cells. For the S2 cell ChIP-chip data, we used data from the following paper: Muse GW, Gilchrist DA, Nechaev S, Shah R, Parker JS, Grissom SF, Zeitlinger J, Adelman K: RNA polymerase is poised for activation across the genome. /Nat Genet /2007, 39(12):1507-1511. The accession number for this data is: GSE6714. Overall Design: ChIP-seq: Profiling chromatin modifications using antibodies against 3 histone modifications and RNA Pol II in S2 cells Profiling chromatin structure in bam testis using antibodies against 3 histone modifications and RNA Pol II RNA-seq: Profiling transcriptome of S2 cells using RNA-seq Contact: Name: Dustin E Schones Organization: City of Hope Deparment: Cancer Biology Address: 1500 E Duarte Rd. Duarte CA 91010 USA Email: dschones@coh.org Organization: GEO Address: USA