NEXSON
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1163030_1.fastq.gz | Fastqsanger.gz | |||
| ERR1163030_2.fastq.gz | Fastqsanger.gz | |||
| ERR1163040_1.fastq.gz | Fastqsanger.gz | |||
| ERR1163040_2.fastq.gz | Fastqsanger.gz | |||
| ERR1163031_1.fastq.gz | Fastqsanger.gz |
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Project description:We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites. Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For this analysis, seven samples from HeLa S3 cells were included: RNA Polymerase II (GEO accession GSM320734), Sono-Seq/Input DNA (small fragments) that was size selected at 100-350 bp (GEO accession GSM320735), Sono-Seq/Input DNA (large fragments) size selected between 350-800 bp, naked DNA, normal mouse IgG, Sono-Seq/Input DNA stimulated with interferon-gamma (GEO accession GSM320737), and MNase-digested DNA. Two replicates were used for MNase-digested DNA and Sono-Seq/Input DNA (large fragments) whereas three replicates were used for all other samples. Naked DNA was used as a reference for scoring peaks.
2008-12-18 | E-GEOD-14022 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing. Using High-resolution X-ChIP-seq we determined the genome-wide binding profile of various DNA binding proteins.
2015-06-12 | E-GEOD-67454 | biostudies-arrayexpress
Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting. Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.
2013-07-01 | E-GEOD-48431 | biostudies-arrayexpress
Project description:We found that sonication of crosslinked chromatin produces breaks at non-random sites in DNA and can be used to map sites of high chromatin accessibility when combined with high-throughput tag sequencing using the GA II platform from Illumina. This technique, which we named Sono-Seq, can be a simple and broadly applicable method for mapping many open chromatin sites. Furthermore, these results give insights into reference sample types, such as Input DNA, normal IgG ChIP DNA, MNase-digested DNA, and naked DNA, that have been used in ChIP-chip and ChIP-Seq experiments. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2008-12-18 | GSE14022 | GEO
Project description:Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited such as highly pure cell populations or early developmental stages of mammalian preimplantation embryo where only few hundred cells might be available. Numerous attempts have been made to reduce the number of cells needed for successful ChIP-seq experiment, however, the developed methods are often complex, laborious or not sensitive enough. Here we describe a new simple method called Restrictase Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables to obtain high quality genome-wide histone modification profiles from as few as 100 cells. The method is simple, cost-effective, takes one day to complete and can potentially be automated. We subsequently use the novel method to derive the first genome-wide maps of histone H3K4me3 and H3K27me3 modifications of inner cell mass (ICM) and trophoectoderm (TE) of bovine blastocyst stage embryos.
2019-11-15 | GSE103734 | GEO
Project description:We developed an affinity purification approach to isolate tagged nuclei in mice (similar to INTACT; [Deal R.B. and Henikoff S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18,1030-1040. (2010)]) and used it to characterize genome-wide patterns of transcription, DNA methylation, and chromatin accessibility in 3 major neuron classes of the neocortex (excitatory pyramidal neurons, parvalbumin (PV)-positive GABAergic interneurons, and vasoactive intestinal peptide (VIP)-positive GABAergic interneurons). By combining cell purification and integrative analysis, our findings relate the phenotypic and functional complexity of neocortical neurons to their underlying transcriptional and epigenetic diversity. RNA-seq, MethylC-seq, ATAC-seq, and ChIP-seq for histone modifications using INTACT-purified nuclei from the mouse neocortex
2015-06-17 | E-GEOD-63137 | biostudies-arrayexpress
Project description:Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution and newer techniques require significant experimental alterations and complex bioinformatics. Here we build upon our high-resolution crosslinking ChIP-seq (X-ChIP-seq) method and compare it to existing methodologies. By using micrococcal nuclease, which has both endo- and exo-nuclease activity to fragment the chromatin and thereby generate precise protein-DNA footprints, high-resolution X-ChIP-seq achieves single base pair resolution of transcription factor binding. A significant advantage of this protocol is the minimal alteration to the conventional ChIP-seq workflow and simple bioinformatic processing.
2015-06-12 | GSE67454 | GEO
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
2020-02-14 | MTBLS1320 | MetaboLights
Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting.
2013-07-01 | GSE48431 | GEO
Project description:Chromatin immunoprecipitation (ChIP) has been a cornerstone for epigenetic analyses over the last decades, but even coupled to sequencing approaches (ChIP-seq), it is ultimately limited to one protein at a time. In a complementary effort, we here combined ChIP with label-free quantitative (LFQ) mass spectrometry (ChIP-MS) to interrogate local chromatin compositions. We demonstrate the versality of our approach at telomeres, with transcription factors, in tissue and by dCas9-driven locus-specific enrichment.
2024-03-05 | PXD039627 | Pride