EXPERIMENT_TITLE: GSM2861708: HSPC_HiC; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: One to five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature. After nuclei permeabilization, DNA was digested with MboI, and digested fragments were labeled using biotinylated d-ATP and ligated. After reverse crosslinking, ligated DNA was purified and sheared to a length of ∼400 bp and biotin labeled DNA fragments were pulled down with streptavidin beads and prepped for Illumina sequencing. Sequencing libraries were constructed according to previous publication Science 326, 289-93 (2009)
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We present the high resolution HiC study of genome folding in primary cells, specifically hematopoietic stem and progenitor cells. We investigated the relationship of chromosomal contacts with other epigenetic marks, particularly DNA methylation and histone modifications which is known to be important for appropriate stem cell differentiation. Overall design: We used in situ Hi-C to probe relationship of chromosomal contacts and epigenetic modification.
SAMPLE_TITLE: HSPC_HiC
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "CD34+CD38-"}, {"TAG": "cell type", "VALUE": "Human Hematopoietic Stem/Progenitor Cells"}, {"TAG": "cell surface marker", "VALUE": "CD34+CD38-"}]
Pool_Member_@attributes_sample_title: HSPC_HiC
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