{"database":"ENA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Biochemistry, University of Vermont"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA345508"],"scientific_name":["Homo sapiens"],"tag":["xref:PubMed:27627025"],"long_description":["Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix–attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix–associated genome is highly cell-context dependent. Overall design: Microarray expression data for 2 cell lines"],"repository":["ENA"],"additional_accession":[]},"is_claimable":false,"name":"Homo sapiens","description":"Identifying Nuclear Matrix–attached DNA across the Genome (Affymetrix)","dates":{"last_updated":"2025-09-24","first_public":"2016-10-07"},"accession":"PRJNA345508","cross_references":{"GEO":["GSE87669"],"taxon":["9606"],"PubMed":["27627025"]}}