Contributors: Suchit Jhunjhunwala, Brian Egan, Madeline Craske, Paul Labhart, Chih-Chi Yuan, Gulfem D Guler, David Arnott, Tobias Maille, Jennifer Busby, Chisato Henry

Date: 2016-01-31

Drosophila chromatin into human ChIP samples and added a Drosophila-specific...Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila...Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila...ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO ...ChIP-seq data and will improve the quantitative comparison of histone ...Drosophila chromatin into human ChIP samples and added a Drosophila-specific ... Accession Number: GSE64243 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2016-01-31 Summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context. Overall Design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment. Contact: Name: Suchit Jhunjhunwala Organization: Genentech Address: 1 DNA Way, MS-93 South San Francisco CA 94080 USA Email: suchitj@gene.com Organization: GEO Address: USA

Contributors: Matthew Taliaferro, Donald Rio

Date: 2013-09-25

Drosophila nucleus using genome-wide methods in conjunction with RNAi ...ChIP-seq Contact: Name: Matthew Taliaferro Organization: MIT Deparment...Drosophila melanogaster) Organism: Drosophila melanogaster Published...Drosophila S2 cells...Drosophila development. Impor- tantly, both of these activities were independent...Drosophila adults. Moreover, we show that nuclear Argonaute-2 binds to ... Accession Number: GSE51134 Platform: GPL15334: Illumina HiSeq 1000 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2013-09-25 Summary: 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. Overall Design: Input chromatin, 2 replicates of Ago2 ChIP-seq Contact: Name: Matthew Taliaferro Organization: MIT Deparment: Biology Address: 77 Massachusetts Ave Cambridge MA 02144 USA Organization: GEO Address: USA

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

Date: 2012-02-27

Drosophila ORC2p); Developmental Stage Embryo 4-7h Contact: Name: DCC...CHIP-seq. BIOLOGICAL SOURCE: Strain: Oregon-R(official name : Oregon-R-modENCODE...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE36106 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-02-27 Summary: modENCODE_submission_4192 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: Strain: Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); Developmental Stage: Embryo 4-7h; Genotype: wild type; EXPERIMENTAL FACTORS: Strain Oregon-R(official name : Oregon-R-modENCODE genotype : wild type ); read length (read_length) ; Antibody dORC2 (target is Drosophila ORC2p); Developmental Stage Embryo 4-7h 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: Alexander (Garrett) Garruss, Alexander S Garruss, Hans-Martin Herz, Ali Shilatifard

Date: 2012-12-01

ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq...Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila...Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1...ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1,...Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax...Drosophila S2 Cells. ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in...Drosophila Trithorax-related, the Drosophila homolog of Mll3/Mll4...Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila...Drosophila melanogaster) Organism: Mus musculus Published on 2012-12 ... Accession Number: GSE41440 Platform: GPL13112: Illumina HiSeq 2000 (Mus musculus) GPL13304: Illumina HiSeq 2000 (Drosophila melanogaster) Organism: Mus musculus Published on 2012-12-01 Summary: Mono-methylation of histone H3 on lysine 4 (H3K4me1) and acetylation of histone H3 on lysine 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and enhancers. Although in yeast all H3K4 methylation patterns including H3K4me1 are implemented by Set1/COMPASS, there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac in various tissues. Assays with the cut wing margin enhancer imply a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrates that Trr is required for H3K4me1 and H3K27ac on chromatin signatures that resemble the histone modification patterns described for enhancers. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 mono-methyltransferase Trr, and the H3K27 demethylase, UTX, cooperate to regulate the transition from inactive/poised to active enhancers. Overall Design: ChIP-seq of Trr, LPT, UTX in Drosophila S2 Cells. ChIP-seq of H3K4me1, H3K4me3, H3K27ac, H3K27me3 in WT and Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila S2 cells. ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq of H3K4me1 and H3K27me3 in MLL1(+/+), MLL1(-/-), MLL3(+/+), and MLL3(-/-) Mouse Embryonic Fibroblasts (MEFs). Contact: Name: Alexander (Garrett) Garruss Organization: Stowers Institute for Medical Research Laboratory: Shilatifard Address: 1000 East 50th Street Kansas CIty Missouri 64110 USA Email: asg@stowers.org Organization: GEO Address: USA

Contributors: Barbara M Bryant, Brian Egan, Paul Labhart, Chih-Chi Yuan, Feng Zhao, Charlie Hatton, Patrick Trojer

Date: 2016-12-01

Drosophila chromatin into human ChIP samples and added a Drosophila-specific...Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila...Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila...ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO ...ChIP-seq data and will improve the quantitative comparison of histone ...Drosophila chromatin into human ChIP samples and added a Drosophila-specific ... Accession Number: GSE63494 Platform: GPL16791: Illumina HiSeq 2500 (Homo sapiens) Organism: Homo sapiens Published on 2016-12-01 Summary: This study outlines a method that dramatically alters the interpretation of ChIP-seq data and will improve the quantitative comparison of histone modification maps across biological contexts or across various conditions within a given biological context. Overall Design: We introduced a small fraction of Drosophila chromatin into human ChIP samples and added a Drosophila-specific antibody as a means to consistently precipitate Drosophila chromatin as a minor fraction of the total ChIP DNA. The Drosophila ChIP-seq tags are used to normalize the human ChIP-seq data from DMSO and EZH2 inhibitor-treated samples. Employing this strategy, a substantial reduction in H3K27me3 levels is observed across the genome upon EZH2 inhibitor treatment. Contact: Name: Barbara M Bryant Organization: Constellation Pharmaceuticals Address: 215 First Street Cambridge MA 02142 USA Email: barbara.bryant@constellationpharma.com Phone: 617-714-0561 Organization: GEO Address: USA

Contributors: Gan Q, Schones DE, Ho Eun S, Wei G, Cui K, Zhao K, Chen X

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 S2 cells to perform ChIP-seq and RNA-seq and compare the results ... 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. 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

Contributors: Xin Chen, Lijuan Feng, Zhen Shi

Date: 2017-01-20

Drosophila melanogaster Published on 2017-01-20 Summary: With the ChIP-seq...ChIP-seq, we used fly testis expressing GFP-tagged E(Pc) specifically ...Drosophila melanogaster Published on 2017-01-20 Summary: With the ChIP-seq...ChIP-seq with GFP antibody was performed. For RNA-seq, RNA was purified...Drosophila melanogaster) GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster ... Accession Number: GSE93828 Platform: GPL16479: Illumina MiSeq (Drosophila melanogaster) GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-01-20 Summary: With the ChIP-seq experiment, we identified direct target genes of E(Pc) specifically in somatic gonadal cells. We found that the E(Pc)-binding genes are enriched with signaling pathway components, consistent with our functional data showing prevailing germline defects even when E(Pc) function is exclusively compromised in somatic gonadal cells. In addition, we also performed RNA-seq to compare transcriptomes between E(Pc) knockdown testes and control testes. Overall Design: For ChIP-seq, we used fly testis expressing GFP-tagged E(Pc) specifically in somatic gonadal cells by Tj promoter driven GAL4>UAS system. ChIP-seq with GFP antibody was performed. For RNA-seq, RNA was purified from Tj-Gal4 or Tj-Gal4/+; UAS-E(Pc) shRNA/+ testes. Contact: Name: Xin Chen Organization: The Joihns Hopkins University Laboratory: Chen Deparment: Biology Address: 3400 N Charles St baltimore MD 21218 USA Email: xchen32@jhu.edu Organization: GEO Address: USA

Contributors: unknown

Date: 2012-12-11

ChIP-Seq profiles of MSL1, MSL2, MSl3, MOF, MLE, H4K16ac and RNA Polymerase...Drosophila S2 cells. 1-3 biological replicates per experiment. Performed...Drosophila S2 cells...Drosophila S2 cells MSL1, MSL2, MSL3, MOF, MLE, H4K16ac and RNA Polymerase ... ChIP-Seq profiles of MSL1, MSL2, MSl3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 in Drosophila S2 cells MSL1, MSL2, MSL3, MOF, MLE, H4K16ac and RNA Polymerase II phosphorlyated on Serine 5 ChIP in Drosophila S2 cells. 1-3 biological replicates per experiment. Performed in single-read and paired-end read mode.

Contributors: Mattias Mannervik, Ann Boija, Per Stenberg

Date: 2015-11-06

Drosophila S2 cells and compared it to modENCODE data. This shows that...ChIP seq in Drosophila S2 cells using two different antibodies against...Drosophila melanogaster) Organism: Drosophila melanogaster Published...ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data...Drosophila S2 cells ... Accession Number: GSE64464 Platform: GPL14601: AB SOLiD 4 System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2015-11-06 Summary: CREB-binding protein (CBP, also known as nejire) is a transcriptional co-activator that is conserved in metazoans. We have generated CBP ChIP-seq data from Drosophila S2 cells and compared it to modENCODE data. This shows that CBP is bound at genomic sites with a wide range of functions. As expected, we find that CBP is bound at active promoters and enhancers. In addition, we find that the strongest CBP sites in the genome are found at Polycomb Response Elements embedded in histone H3 lysine 27 trimethylated (H3K27me3) chromatin, where they correlate with binding of the Pho repressive complex. Interestingly, we find that CBP also binds to most insulators in the genome. At a subset of these, CBP may regulate insulating activity, measured as the ability to prevent repressive H3K27 methylation from spreading into adjacent chromatin. Overall Design: ChIP seq in Drosophila S2 cells using two different antibodies against CBP (nejire), one raised in rabbit against amino acids 2540-3190 (CBP rb), and one raised in guinea-pig against amino acids 1-178 (CBP gp) Contact: Name: Mattias Mannervik Organization: Stockholm University Laboratory: Mattias Mannervik Deparment: Molecular Biosciences, the Wenner-Gren Institute Address: Arrheniuslaboratories E3 Stockholm 10691 Sweden Email: mattias.mannervik@su.se Organization: GEO Address: USA

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

Date: 2012-06-07

CHIP-seq. BIOLOGICAL SOURCE: Cell Line: CME-W1-Cl.8+; Tissue: dorsal mesothoracic...Drosophila melanogaster) Organism: Drosophila melanogaster Published ... Accession Number: GSE38559 Platform: GPL9058: Illumina Genome Analyzer (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2012-06-07 Summary: modENCODE_submission_4352 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: Antibody Anti-RNA polymerase II clone CTD4H8 (target is RNA polymerase II) 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