Contributors: Oscar Reina Garcia, Roman Kessler, Fernando Azorín

Date: 2015-05-01

Drosophila melanogaster) Organism: Drosophila melanogaster Published...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: unknown

Date: 2013-05-23

ChIP-seq for Pol II in various Drosophila embryos...Drosophila embryos...Chip-seq using mutant embryos for the dorsal gradient. We used two population ... In order to idetify paused promoters in vivo, we performed tissue specific Pol II Chip-seq using mutant embryos for the dorsal gradient. We used two population of cells, either dorsal ectoderm cells (gd7 embryos) or mesodermal cells (Toll10b) embryos. ChIP-seq for Pol II in various Drosophila embryos

Contributors: unknown

Date: 2012-08-01

Drosophila neurons [ChIP-Seq] Refer to individual Series...Drosophila neurons [ChIP-Seq] Refer to individual Series...Drosophila neurons...Drosophila neurons [RNA-Seq] GSE37032: Cell type-specific chromatin profiling...Drosophila neurons [RNA-Seq] GSE37032: Cell type-specific chromatin profiling ... This SuperSeries is composed of the following subset Series: GSE37027: Cell type-specific gene expression profiling of Drosophila neurons [RNA-Seq] GSE37032: Cell type-specific chromatin profiling of Drosophila neurons [ChIP-Seq] Refer to individual Series

Contributors: Kevin P. White, Xiaochun Ni, Kevin P White

Date: 2012-11-08

Drosophila melanogaster Published on 2012-11-08 Summary: This is a dataset...Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila...Drosophila pseudoobscura) GPL11000: Illumina Genome Analyzer (Drosophila...Drosophila melanogaster) GPL9394: Illumina Genome Analyzer (Drosophila...Drosophila species : Drosophila melanogaster, Drosophila simulans, Drosophila...Drosophila species: First, triplicate ChIP-seq data of CTCF (CCCTC binding...Drosophila white prepupa on Illumina Genome Analyzer ... 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

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: David Scott Gilmour, Jian Li, David S Gilmour

Date: 2013-08-13

Drosophila S2R+ cells...Drosophila S2R+ cells Overall Design: Polyclonal antibody raised against...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila cells with formaldehyde, lysing the cells, and shearing DNA ... Accession Number: GSE49842 Platform: GPL9521: AB SOLiD System 2.0 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-08-13 Summary: The genomic distribution of a novel transcription factor called M1BP was determined in Drosophila S2R+ cells Overall Design: Polyclonal antibody raised against M1BP was used to immunoprecipitate M1BP-DNA adducts generated by treating Drosophila cells with formaldehyde, lysing the cells, and shearing DNA by sonication. Immunoprecipitated DNA was sequenced using the AB SOLiD system. Contact: Name: David Scott Gilmour Organization: Penn State University Laboratory: Gilmour Deparment: Biochemistry and Molecular Biology Address: 465 North Frear University Park Pennsylvania 16802 USA Email: dsg11@psu.edu Phone: 814-863-8905 Organization: GEO Address: USA

Contributors: Saverio Brogna

Date: 2016-11-22

ChIP-seq Y14 Overall Design: Y14 ChIP-seq in S2 cells Contact: Name:...Drosophila melanogaster...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE84595 Platform: GPL14601: AB SOLiD 4 System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2016-11-22 Summary: ChIP-seq Y14 Overall Design: Y14 ChIP-seq in S2 cells Contact: Name: Saverio Brogna Organization: University Birmingham Address: Edgbaston Birmingham United Kingdom Email: s.brogna@bham.ac.uk Organization: GEO Address: USA

Contributors: Schuettengruber B, Oded Elkayam N, Sexton T, Entrevan M, Stern S, Thomas A, Yaffe E, Parrinello H, Tanay A, Cavalli G

Date: 2014-10-20

Drosophila species We validate few cases of PRE divergence that shows ...ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate ...Drosophila species. We demonstrate an extremely high conservation of Polycomb...Drosophila...Drosophila species...ChIP-seq analysis of histone marks and chromatin associated factors across ... We report the evolutionary behaviour of Polycomb group proteins, their recruitment factors and their underlying sequences by performing ChIP-seq analysis in 4-5 different Drosophila species. We demonstrate an extremely high conservation of Polycomb repressive domains across Drosophila species We validate few cases of PRE divergence that shows that cis-driven PRE evolution is a rare event. We further show that PHO recruitment to Polycomb domains is evolutionarily robust to motif changes and that PRC1 stabilizes binding of its key recruiter ChIP-seq analysis of histone marks and chromatin associated factors across 4-5 Drosophila species

Contributors: DCC modENCODE, David MacAlpine, Heather MacAlpine, Joseph Prinz

Date: 2012-06-07

Drosophila ORC2p); read length (read_length) Contact: Name: DCC modENCODE...CHIP-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... 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

Contributors: unknown

Date: 2013-09-25

Drosophila nucleus using genome-wide methods in conjunction with RNAi ...ChIP-seq...Drosophila S2 cells...Drosophila development. Impor- tantly, both of these activities were independent...Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to ... Transcription and pre-mRNA alternative splicing are highly regulated processes that play major roles in modulating eukaryotic gene expression. It is increasingly apparent that other pathways of RNA metabolism, including small RNA biogenesis, can regulate these processes. However, a direct link between alternative pre- mRNA splicing and small RNA pathways has remained elusive. Here we show that the small RNA pathway protein Argonaute-2 (Ago-2) regulates alternative pre-mRNA splicing patterns of specific transcripts in the Drosophila nucleus using genome-wide methods in conjunction with RNAi in cell culture and Ago-2 deletion or catalytic site mutations in Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to specific chromatin sites near gene promoters and negatively regulates the transcription of the Ago-2-associated target genes. These transcriptional target genes are also bound by Polycomb group (PcG) transcriptional repressor proteins and change during development, implying that Ago-2 may regulate Drosophila development. Impor- tantly, both of these activities were independent of the catalytic activity of Ago-2, suggesting new roles for Ago-2 in the nucleus. Finally, we determined the nuclear RNA-binding profile of Ago-2, found it bound to several splicing target transcripts, and identified a G-rich RNA-binding site for Ago-2 that was enriched in these transcripts. These results suggest two new nuclear roles for Ago-2: one in pre-mRNA splicing and one in transcriptional repression. Input chromatin, 2 replicates of Ago2 ChIP-seq