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241612 results
  • ChIP-seq of H1 human embryonic stem cells (hESCs) to map the global binding profile of EZH2 to investigate the association of PRDM14 binding with the PRC2 in hESCs
    An experiment was performed to map the global binding profile of EZH2 in human embryonic stem cells (hESCs). How the Polycomb Repressive Complex 2 (PRC2) is recruited to the DNA in hESC remains largely unknown. Previous studies on the transcription factor PRDM14 suggested that PRDM14 plays a repressive role in hESCs. Here, we mapped the global binding profile of EZH2 in hESC to investigate the association of PRDM14 binding with the PRC2 in hESCs. EZH2 binding is found to be enriched in PRDM14 binding sites. The PRC2 dependent repressive role of PRDM14 is further supported by the strong correlation of PRDM14 binding with the repressive histone modification H3K27me3.
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  • Cactophilic Drosophila and Opuntia
    Collection of cactophilic Drosophila for genetics research. As well as Drosophila collection, locations of Opuntia were recorded.
    • Dataset
  • Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq
    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. This SuperSeries is composed of the following subset Series: GSE15422: ChIP-chip of H3K9me3 in Drosophila at different time points of development GSE15423: ChIP-chip of H3K27me3 in Drosophila at different time points of development GSE15424: ChIP-chip of H3K4me3 in Drosophila at different time points of development GSE15425: ChIP-chip of H3K4me1 in Drosophila at different time points of development GSE15426: ChIP-chip of H3K9Ac in Drosophila at different time points of development GSE15427: ChIP-chip of CBP/p300 in Drosophila at different time points of development GSE15430: ChIP-chip of H3K27Ac in Drosophila at different time points of development GSE16013: Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq GSE16702: ChIP-chip of PolII in Drosophila at different time points of development GSE18068: Genome-wide maps of chromatin state in staged Drosophila embryos, RNA-seq For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf 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.
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  • Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-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
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  • CEL-Seq-pipeline: CEL-Seq2 pipeline version 1.0
    CEL-Seq2 pipeline version 1.0
    • Software/Code
  • ChIP-seq of Atrophin in Drosophila S2 cells
    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
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  • The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis
    This dataset contains zebrafish (Danio rerio) raw RNA and ChIP (paired-end) sequencing data: NDC-TLF-3dpf-repl*: 5 biological replicates of RNA-seq data from 3dpf wild-type (TL background) whole embryo lysates TLF-3dpf-replicate*: 3 biological replicates of RNA-seq data from 3dpf wild-type (TL background) whole embryo lysates WT[12]-3dpf-ChIP-H3K27me3*: 2 biological replicates of H3K27me3 ChIP-seq data from 3dpf wild-type (TU/TF mixed background) whole embryo lysates WT[12]-3dpf-H3K27me3-spikein*: 2 biological replicates of H3K27me3 ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates WT[12]-3dpf-Rnf2-spikein*: 2 biological replicates of Rnf2 ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates WT2-3dpf-input-spikein*: input ChIP-seq data (with Drosophila H2Ay spike in) from 3dpf wild-type (TU/TF mixed background) whole embryo lysates
    • Dataset
  • Drosophila dKDM5/LID regulates H3K4me3 dynamics at the transcription start site of actively transcribed developmental genes
    This SuperSeries is composed of the following subset Series: GSE26895: Drosophila LID RNAi gene expression profiling GSE27078: LID ChIP-Seq in wild type, and H3K4me3 ChIP-Seq in wild type and lid RNAi Drosophila melanogaster GSE40599: POLIISER5 and POLIISER2 ChIP-Seq in mutant RNAi LID Drosophila Melanogaster Refer to individual Series
    • Software/Code
    • Tabular Data
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    • File Set
  • Atrophin (Atro) ChIP-seq data from Drosophila S2 cells
    Accession Number: GSE87471 Platform: GPL14762: AB SOLiD System (Drosophila melanogaster) Organism: Drosophila melanogaster Published on 2017-03-16 Summary: We performed ChIP-seq with Drospohila Atrophin (also known as Grunge) antibody using S2 cell chromatin. Atro ChIP-seq peaks are most frequent in promoters and introns of highly expressed, paused genes in S2 cells, including several components of developmental signaling pathways. The Atro peaks overlap significantly with GAGA factor (Trithorax-like, Trl). Overall Design: ChIP-seq in Drosophila S2 cells with an antibody (4H6) raised against the peptide SRQSPLHPVP in the C-terminus of Drospohila Atro 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
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  • A ChIP-seq spike-in method enables detection of global histone modification changes across the genome
    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
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