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Suz12, EZH2, EED1, H3me3K27, H3me3K9 and RNA Pol II target promoters in mouse F9 and mES cells

ABSTRACT: For each sample a matched total was prepared in parallel. For each biological replicate the cells were crosslinked on different days. Amplicons were prepared from each sample and hybridized on mouse 1.5 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

ORGANISM(S): Mus musculus

PROVIDER: GSE4908 | GEO | 2006/06/06

SECONDARY ACCESSION(S): PRJNA95909

REPOSITORIES: GEO

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Suz12, EZH2 and H3me3K27 binding sites in F9 cells

Project description:Suz12 samples are biological replicates from F9 cells crosslinked on different days. EZH2 and H3me3K27 samples are from the same batch of crosslinked cells as Suz12 replicate 2. For each sample matched total was prepared in parallel. Amplicons were made and hybridized on custom genomic tiling arrays. Keywords: ChIP-chip

2006-06-06 | GSE4907 | GEO

Oct4 and RNA Pol II target promoters in Ntera cells

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Suz12 target promoters in Ntera, MCF7 and SW480 cells

Project description:For each sample a matched total was produced in parallel. Amplicons were made from each and hybridized on human 5.0 kb promoter arrays from Nimblegen. Keywords: ChIP-chip

2006-06-06 | GSE4905 | GEO

Suz12, EZH2, EED1, H3me3K27 binding sites in Ntera cells

Project description:All samples are from the same batch of crosslinked Ntera cells with a matched total produced in parallel. Amplicons were made from each and hybridized on ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Keywords: ChIP-chip

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HeLa E2F1 ChIP-chip experiments

Project description:These are three biological replicates. HeLa cells were crosslinked on separate days. In each case, a matched total from the same crosslinking was produced in parallel. Amplicons were made from each and hybridized onto ENCODE region tiling arrays. Two color arrays were used; ChIP was red, Total was green. Goal was determination of E2F1 binding sites in HeLa cells by using ChIP-chip methodology. See Farnham Lab website for downloadable protocol for ChIP or supplementary file (Chip_protocol.txt) below. NimbleGen performed all array processing. See NimbleGen website for information on array procedures.

2010-07-01 | E-GEOD-4306 | biostudies-arrayexpress

HeLa E2F1 ChIP-chip experiments

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<i>Caenorhabditis elegans</i> MES-3 is a highly divergent ortholog of the canonical PRC2 component SUZ12.

Project description:Polycomb Repressive Complex 2 (PRC2) catalyzes the mono-, di-, and trimethylation of histone protein H3 on lysine 27 (H3K27), which is strongly associated with transcriptionally silent chromatin. The functional core of PRC2 is highly conserved in animals and consists of four subunits. One of these, SUZ12, has not been identified in the genetic model Caenorhabditis elegans, whereas C. elegans PRC2 contains the clade-specific MES-3 protein. Through unbiased sensitive sequence similarity searches complemented by high-quality structure predictions of monomers and multimers, we here demonstrate that MES-3 is a highly divergent ortholog of SUZ12. MES-3 shares protein folds and conserved residues of key domains with SUZ12 and is predicted to interact with core PRC2 members similar to SUZ12 in human PRC2. Thus, in agreement with previous genetic and biochemical studies, we provide evidence that C. elegans contains a diverged yet evolutionary conserved core PRC2, like other animals.

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Pol II Ser7phospho ChIP-seq in mES cells

Project description:RNA Polymerase II transcribes protein-coding and many non-coding RNA genes in eukaryotes. The largest subunit of RNA Polymerase II, Rpb1, contains a hepta-peptide repeat on its C-terminal tail with three potential phosphorylation sites (Serine 2, Serine 5 and Serine 7). Mammalian Rpb1 contains 52 repeats. The phosphorylation events are catalyzed by specific protein kinases where the phosphorylation of specific residues is coupled to the transcription cycle. For example, the Cdk7 subunit of TFIIH phosphorylates both Serine 5 and Serine 7 during intiation and the Cdk9 subunit of P-TEFb phosphorylates Serine 2 during the transition into productive elongation. The dataset presented here is the genome-wide distribution of RNA Pol II with Serine 7 of the CTD phosphorylated in murine embryonic stem cells. This data, in addition to phospho-specific datasets generated in the same cell type in Rahl et al. Cell 2010 and Seila et al. Science 2008, represents the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II. An antibody specific to RNA Pol II Serine 7 phosphorylated CTD (gift of Dirk Eick; Chapman et al. Science 2008) was used to enrich for DNA fragments associated with this Pol II isoform in murine embryonic stem cells. DNA was purified and prepared for Illumina/Solexa sequencing following their standard protocol. This is a single dataset but together with datasets from Rahl et al. Cell 2010 and Seila et al. Science 2008, these datasets represent the genome-wide distribution of multiple RNA Pol II isoforms in murine embryonic stem cells: total Pol II, hypophosphorylated CTD Pol II, Serine 2 phosphorylated CTD Pol II, Serine 5 phosphorylated CTD Pol II and Serine 7 phosphorylated CTD Pol II.

2010-05-20 | E-GEOD-21917 | biostudies-arrayexpress

Expression data from rice leaves treated or not with fungal elicitors and high-throughput pyrosequencing of endogenous small RNAs from Oryza sativa

Project description:High-throughput sequencing of small RNAs from rice was used to identify distinct miRNAs that are responsive to elicitors from the fungal pathogen Magnaporthe oryzae. [Expression profiling by array] We used microarrays to determine the expression behaviour of target genes for elicitor-regulated miRNAs. [High throughput sequencing] High-throughput sequencing of rice small RNAs was performed in two different tissues, leaves and roots, and two different time point of elicitor treatment, 30' and 2h Amplicons were prepared by 5´and 3´adaptor ligation in which the 5'-adaptor contained a 'barcode' consisting of a 4-nucleotide identifier sequence for each sample. The libraries containing unique barcodes were combined and subjected to pyrosequencing (454 Life SciencesTM, Roche)

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MOYO-S and MOYO-R responsive genes to dengue-2 infection at 3hr and 18hr post-infection times

Project description:We conducted a genome-wide survey of genes in Ae. aegypti females that are transcriptionally responsive upon challenge with dengue virus (serotype-2). The array was designed with 60-mer oligos specific to 16,092 gene transcripts of gene build AaegL1.1 (www. vectorbase.org). The hybridizations were performed at NimbleGen. We provided total RNA purified from the infected and control samples to NimbleGen. To identify dengue-specific transcription response (DTR) genes of MS and MR females upon infection with DENV2-JAM1409, a total of 15 independent samples (12 test samples and 3 control samples) were used for array hybridizations. These consisted of four DENV2 infected samples (MS-3hr, MR-3hr, MS-18hr and MR-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Three independent biological replicates were prepared for each of the above five samples were used for hybridizations.

2011-09-30 | GSE16563 | GEO

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