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Nucleosome map of the IMR90 fibroblast cell line

ABSTRACT: We produced a map of nucleosome positions in IMR90 by sequencing the ends of MNase-digested chromatin fragments.

ORGANISM(S): Homo sapiens

PROVIDER: GSE21823 | GEO | 2011/04/01

SECONDARY ACCESSION(S): PRJNA127079

REPOSITORIES: GEO

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Nucleosome map of the IMR90 fibroblast cell line

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

Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

Project description:Human UL3 cells (U20S derivatives containing GR and an MMTV-luc transgene) were treated with dexamethasone for 0, 1 or 4 hrs. Chromatin was harvested, digested with to ~70% mononucleosomes with MNase, and isolated mononucleosome fragments were used to probe custom Nimblegen genomic tiling microarrays. In addition, human HL60 cells were treated with or without DMSO to induce granulocyte differentiaton, and mononucleosome positions mapped. MNase digested bare DNA fragments of ~500 bp average length from UL3 cells was used as a control.

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Nucleosome mapping data from GR and cell-cycle regulated genes in human cell lines

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Nucleosome positioning in the IMR90 cell line

Project description:Micrococcal nuclease (Mnase) treatment and sequencing of mononucleosomal DNA One single sample in the IMR90 fibroblast cell line

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Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq]

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Quantitative MNase-seq accurately maps nucleosome occupancy levels

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.

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DNA Methylation in IMR90 cells

Project description:DNA methylation was measured by MBD2 enrichment of DNA fragments in IMR90. A statistical model was developed to estimate absolute methylation levels, and compared to whole genome bisulfite sequencing results (Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature)

2012-11-30 | GSE38679 | GEO

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