Nucleosome positioning in the IMR90 cell line
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE44985 | GEO | 2015/03/03
SECONDARY ACCESSION(S): PRJNA192702
REPOSITORIES: GEO
Similar Datasets
Project description:Micrococcal nuclease (Mnase) treatment and sequencing of mononucleosomal DNA One single sample in the IMR90 fibroblast cell line
2015-03-03 | E-GEOD-44985 | biostudies-arrayexpress
Project description:We produced a map of nucleosome positions in IMR90 by sequencing the ends of MNase-digested chromatin fragments. IMR90 cells were grown in culture, about 1E6 cells were isolated and digested using micrococcal nuclease (MNase). Mononucleosomes were gel-selected and fragment ends were sequenced using the Illumina GAIIx sequencing platform.
2011-04-01 | E-GEOD-21823 | biostudies-arrayexpress
Project description:Nucleosomal DNA was prepared using Simple ChIP Enzymatic Chromatin IP Kit according to manufacturer’s instruction. Briefly, Nuclei were isolated from purified Ter119 negative or in vitro cultured erythroblasts. Cross-linked native chromatin was then digested with MNase into mononucleosomal DNA. Sequencing libraries were generated from nucleosomal DNA, and sequencing was carried out using the Illumina system according to the manufacturer’s specification. In this study, we purified chromatin from in vitro cultured mouse fetal liver erythroblasts on day 0, day 1, and day 2. The chromatins were digested by micrococcal nuclease to make mononucleosomal products, which were further analyzed by next generation sequencing analysis. We aim to determine the dynamic changes of nucleosome during terminal erythropoiesis.
2014-10-01 | E-GEOD-55825 | biostudies-arrayexpress
Project description:To analyse nucleosome positioning and occupancy we performed micrococcal nuclease digestion of Arabidopsis wild type (Col-0) chromatin and gel purified the resulting ~150 bp mononucleosomal DNA band. This DNA was used to generate a library and paired-end sequencing performed (MNase-seq). To further examine influence of SWR1 chromatin remodelling complex and DNA methylation on nucleosome occupancy, we repeated MNase-seq in Aarabidopsis arp6 and met1 mutant.
2017-06-05 | E-MTAB-5042 | biostudies-arrayexpress
Project description:To measure nucleosome positions on a genomic scale, we developed a high-throughput DNA microarray method to identify nucleosomal and linker DNA sequences based on susceptibility of linker DNA to micrococcal nuclease. Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest. Keywords = nucleosome Keywords = yeast Keywords = tiling microrray Keywords: repeat sample
2005-07-14 | GSE2563 | GEO
Project description:To measure nucleosome positions on a genomic scale, we developed a high-throughput DNA microarray method to identify nucleosomal and linker DNA sequences based on susceptibility of linker DNA to micrococcal nuclease. Nucleosomal DNA was isolated and labeled with Cy3 fluorescent dye (green), and mixed with Cy5-labeled total genomic DNA (red). This mixture was hybridized to microarrays printed with overlapping 50mer oligonucleotide probes tiled across chromosomal regions of interest. Keywords = nucleosome Keywords = yeast Keywords = tiling microrray
2010-06-09 | E-GEOD-2563 | biostudies-arrayexpress
Project description:Open chromatin provides access to a wide spectrum of DNA binding proteins for DNA metabolism processes such as transcription, repair, recombination, and replication. In this regard, open chromatin profiling has been widely used to identify the location of regulatory regions, including promoters, enhancers, insulators, silencers, replication origins, and recombination hotspots. Regulatory DNA elements are made accessible by nucleosome-depeleted states. Thus, nucleosome remodelling and modification should be intimately coupled with open chromatin formation and regulation. However, our knowledge of nucleosome regulation is largely limited to promoter regions, which comprise only a subset of all regulatory loci in the genome. In order to examine nucleosome patterns in open chromatin regions, we performed micrococcal nuclease (MNase) sequencing for a laboratory strain of yeast. Nucleosome occupancy profiled by Micrococcal nuclease (MNase) digestion
2013-01-06 | E-GEOD-34923 | biostudies-arrayexpress
Project description:Chromatin mapping using micrococcal nuclease (MNase) has been the standard tool for mapping nucleosomes for >40 years. When coupled with DNA sequencing, MNase-seq can provide base-pair-resolution nucleosome maps. However, determining nucleosome occupancy using MNase-seq has been hampered by its aggressive endo-/exo-nuclease activities, whereby cleavages within linker regions produce oligo- and mono-nucleosomes whereas cleavages within nucleosomes destroy them. Here we introduce a theoretical framework for predicting nucleosome occupancies and an experimental protocol with appropriate spike-in normalization that confirms our theory and provides accurate occupancy levels over an MNase digestion time-course. As expected, DNaseI hypersensitive sites and transcription units are digested by MNase at elevated rates, and the apparent deficiency of nucleosomes at 3’ ends of Drosophila genes is an artifact of MNase preference for AT-rich DNA. Surprisingly, we observed no overall differences between Drosophila euchromatin and heterochromatin, which implies that heterochromatin compaction does not render nucleosomal DNA less accessible than euchromatin.
2019-08-27 | GSE128689 | GEO
Project description:To investigate the relationship between meiotic recombination initiation and H3K4m3 in Arabidopsis, we generated and sequenced H3K4m3 ChIP libraries from meiotic stage floral buds in wild type, arp6 and met1. To produce high-resolution of H3K4m3 mapping, we used micrococcal nuclease (MNase) to digest chromatins that were cross-linked by formaldehyde for ChIP. This experiment provides for H3K4m3 maps with the resolution of mononucleosomal DNA level (~150 bp).
2017-06-05 | E-MTAB-5048 | biostudies-arrayexpress
Project description:To study recombination at the fine-scale we used high-throughput sequencing to analyse >1,000 crossovers within the RAC1 R gene hotspot. This revealed focused intragenic crossovers, overlapping exons encoding the TIR, NBS and LRR domains (RAC1 pollen typing sequencing). To analyse chromatin structure we performed micrococcal nuclease digestion of wild type (Col-0) chromatin and gel purified the resulting ~150 bp mononucleosomal DNA band. This DNA was used to generate a library and paired-end sequencing performed (MNase-seq)
2016-07-15 | E-MTAB-4556 | biostudies-arrayexpress