Contributors: unknown

Date: 2016-07-17

Drosophila species. ChIP seq experiments compare the binding profile of...Drosophila dosage compensation [ChIP-Seq]...ChIP-seq was performed to compare binding the genome-wide binding profile ... ChIP-seq was performed to compare binding the genome-wide binding profile of the CLAMP transcription factor in two different Drosophila species. ChIP seq experiments compare the binding profile of CLAMP in female larvae to identify conservation of its binding sequence.

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: Michael Tolstorukov, E Larschan

Date: 2016-07-17

Drosophila dosage compensation [ChIP-Seq]...Drosophila melanogaster) GPL22022: Illumina HiSeq 2500 (Drosophila miranda...Drosophila species. Overall Design: ChIP seq experiments compare the ...Drosophila melanogaster Published on 2016-07-17 Summary: ChIP-seq was ... Accession Number: GSE83435 Platform: GPL17275: Illumina HiSeq 2500 (Drosophila melanogaster) GPL22022: Illumina HiSeq 2500 (Drosophila miranda) Organism: Drosophila melanogaster Published on 2016-07-17 Summary: ChIP-seq was performed to compare binding the genome-wide binding profile of the CLAMP transcription factor in two different Drosophila species. Overall Design: ChIP seq experiments compare the binding profile of CLAMP in female larvae to identify conservation of its binding sequence. Contact: Name: Michael Tolstorukov Organization: Massachusetts General Hospital Deparment: Molecular Biology Address: 185 Cambridge Street Boston MA 02114 USA Email: tolstorukov@molbio.mgh.harvard.edu 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: unknown

Date: 2013-05-23

ChIP-seq for Pol II in various Drosophila embryos...Chip-Seq in the early fly embryo...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: 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: Herz HM, Mohan M, Garruss AS, Liang K, Takahashi YH, Mickey K, Voets O, Verrijzer CP, Shilatifard A

Date: 2012-12-01

ChIP-seq of LPT and UTX in Trr knock-down Drosophila S2 cells. ChIP-seq...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 Trithorax-related, the Drosophila homolog of Mll3/Mll4...Drosophila S2 cells. ChIP-seq of H3K4me1, H3K27me3 in LPT knock-down Drosophila...Drosophila homolog of mammalian Mll3/4, can function as a major H3K4 mono-methyltransferase ... 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. 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).

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

Date: 2012-11-08

Drosophila species: Drosophila melanogaster, Drosophila simulans and Drosophila...ChIP-seq data of CTCF and RNA-seq data in Drosophila white prepupa on ...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 ... 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: 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...ChIP-seq of endogenous Ago2 in Drosophila S2 cells...Drosophila melanogaster) Organism: Drosophila melanogaster Published...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