Genome-wide analysis of K3K27ac, H2AZ and methylation data in mouse embryonic stem cells
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ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Chieh-Chun Chen
PROVIDER: E-GEOD-34953 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Genome-wide maps of cytosine methylation, cytosine hydroxylmethylation and small non coding RNAs in mouse ES cells and upon guided differentiation to mesoendoderm cells. Mouse embryonic stem cells (E14) were guided differentiated into mesoendoderm lineages by activin-A induction. cells in three time points (day0, day4 and day6) were collected. The genome-wide studies on three cell types were summerized as following: cytosine methylation data were generated using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq); DNA product for 5-hmC_ChIP-seq is generated by a selctive chemical labeling method (Nat. Biotechnol. 2011, 29, 68-72). E14 Day0 data for MRE-seq and MeDIP-seq are released first in previous publication and included in prior series GSE36114 ChIP-seq, 5-hmC-seq, MeDIP-Seq, MRE-Seq, ncRNA-Seq, and RNA-seq on activin-induced differentiating ES cells at 3 time points.
2012-09-22 | E-GEOD-38596 | biostudies-arrayexpress
Project description:Genome-wide analysis of histone modification (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3), protein-DNA binding (TAF1, P300, Pou5f1 and Nanog), cytosine methylation and transcriptome data in mouse and human ES cells and pig iPS cells We generated histone modification data (H2AZ, H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, H3K4me3 and H3K9me3) and protein-DNA binding data (TAF1, P300, Pou5f1 and Nanog) using Chromatin Immunoprecipitation followed by short sequencing (ChIP-seq), cytosine methylation data using methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) and DNA digestion by methyl-sensitive restriction enzymes followed by sequencing (MRE-seq), transcriptome data with RNA short sequencing (RNA-seq) in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation. Examination of 8 histone modifications, 4 protein-DNA binding, cytosine methylation and transcriptome in human embryonic stem cells, mouse embryonic stem cells, pig induced pluripotent stem cells and mouse embryonic stem cells under activin-A-induced-differentiation.
2012-02-28 | E-GEOD-36114 | biostudies-arrayexpress
Project description:Purpose: Description of a spike-adjusting-method (SAM) to normalize ChIP-seq data . Methods: We performed ChIP-seq of POLR3D and POLR2B with mouse liver supplemented with 2.5% of human DNA. Human DNA will be used as an internal control for ChIP-seq quantification. Results: We show that using the SAM for ChIP-seq quantification improve similarity of POLR3D and POLR2B ChIP-seq replicates samples and improve difference between samples originate from different conditions. Conclusions: The SAM improves comparison of ChIP-seq samples, either by increasing similarity between replicates or by emphasise differences between conditions. Chromatin Immuno-precipitations were performed with antibodies directed against POLR3D (Pol III) and POLR2B (Pol II) using mouse liver material supplemented with human DNA. Immuno-precipitated DNA was next sequenced using Illumina HiSeq. Three different concentrations of human spiked DNA were tested for the Pol III ChIP (2.5%, 5% and 10%). We also sequenced the corresponding inputs (crosslinked DNA from mouse liver). Two concentrations of human spiked DNA (5% and 10%) were tested for the Pol 2 ChIP. We also sequenced the corresponding inputs (crosslinked DNA from mouse liver).
2014-04-02 | E-GEOD-52049 | biostudies-arrayexpress
Project description:Purpose: Characterization of the target genes of two versions of the Polymerase III (pol III), one containing POLR3G subunit or POLR3GL subunit, in different tissues. Methods: We performed ChIP_seq of POLR3D and the two variants subunits, POLR3G and POLR3GL in Human IMR90 cells, Mouse liver and Mouse Hepatocarcinoma Hepa 1-6 cells in order to locate and analyse total pol III, POLR3G and POLR3GL-containing pol III in various tissues. Results: We show that POLR3G- as well as POLR3GL-containing pol III are present in cultured cell lines and in normal mouse liver, although the relative amounts of the two forms vary, with the POLR3G-containing pol III relatively more abundant in dividing cells. Both forms of pol III occupy the same target genes, in very constant proportions within one cell line, suggesting that the two forms of pol III have similar function with regard to specificity for target genes. Conclusions: POLR3G and POLR3GL occupy the same target genes, but they are differentially expressed under different conditions and in different cell types. Pol III target genes in human IMR cells, Mouse liver, and Mouse Hepatocarcinoma cells were identified by chromatin Immuno-precipitation followed by deep sequencing using Illumina HiSeq. For Human IMR90 cells, we used antibodies against POLR3D, POLR3G, POLR3GL and BDP1. For Mouse data, we targeted POLR3D, POLR3G and POLR3GL and did ChIP_seq replicates. We also sequenced the corresponding inputs (crosslinked DNA of IMR90 cells, Mouse liver, and Mouse Hepatocarcinoma cells). This represents a total of 20 samples.
2013-10-01 | E-GEOD-47849 | biostudies-arrayexpress
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2014-07-03 | E-GEOD-52939 | biostudies-arrayexpress
Project description:Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest. Targeted genomic enrichment followed by next-generation sequencing dramatically increased the efficiency of mutation discovery in human genomes. Here we demonstrate that these techniques also revolutionize traditional genetic approaches in model systems. We developed a two-step protocol utilizing a traditional bulk-segregant analysis (BSA) approach for positional cloning mutants in phenotype-driven forward genetic screens. First, BSA pools are 'light' sequenced for rough mapping, followed by targeted enrichment and deep-sequencing of the mutant BSA pool for the linked genomic region to fine-map and discover candidate mutations. We applied this method successfully to three Arabidopsis mutants and show that it can be scaled by multiplexing. Similarly, we applied these techniques to a gene-driven reverse genetics method (chemical driven target-selected mutagenesis or TILLING) that is used for generating gene knockouts in a wide range of organisms, including plants, invertebrates and vertebrates. We developed an efficient multiplexed genomic enrichment protocol for pre-barcoded samples. As a proof-of-principle, 770 genes were screened for induced mutations in 30 rats, which identified all but one known variants (30) as well as a large series of novel knockout and missense alleles. Mutations were retrieved at the expected frequency with a the false-positive rate of less than 1 in 6 million basepairs, which is much lower as compared to traditional mutation discovery approaches. Both methods are largely independent of the genome size due to the targeted enrichment and can thus be applied to any genetic model system of interest.
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Project description:This SuperSeries is composed of the following subset Series: GSE31233: Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation that establish T cell identity [ChIP-Seq] GSE31234: Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation that establish T cell identity [RNA-Seq] Refer to individual Series
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2014-12-05 | E-GEOD-63341 | biostudies-arrayexpress
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