EXPERIMENT_TITLE: GSM6261020: Progeria‐167‐DpnII‐P19‐R1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Briefly, 5-20 million cells were fixed with 1% formaldehyde, suspended in cell lysis buffer for permeabilization, and homogenized by douncing.  Samples were then digested overnight with HindIII or DpnII (as indicated per sample).  Ends were filled in with biotin and ligated.  Then, crosslinking was reversed. Biotinylated DNA was pulled down using streptavidin coated magnetic beads and prepared for multiplex sequencing on an Illumina platform using the NEBNext Ultra II kit (NEB). All end preparation, adaptor ligation, and PCR amplification steps were carried out on bead bound DNA libraries.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We investigate the 3D genome alterations in early and late passage progeria (HGPS) using two different patient cell lines and two different healthy adult cell lines. Overall design: Primary skin fibroblast cells from Progeria patients and healthy parents of progeria patients were grown to confluency and crosslinked with 1% formaldehyde.  Hi-C was performed according to protocol specified and paired end reads were sequenced and mapped to the genome to create chromosome contact matrices.
SAMPLE_TITLE: Progeria‐167‐DpnII‐P19‐R1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Skin fibroblast (HGADFN167, Progeria Research Foundation)"}, {"TAG": "enzyme", "VALUE": "DpnII"}, {"TAG": "condition", "VALUE": "HGPS (2036C>T, GLY608GLY)"}, {"TAG": "media", "VALUE": "DMEM,15%FBS,1xNonessentialAA"}, {"TAG": "passage", "VALUE": "Passage 19"}, {"TAG": "hi-c protocol", "VALUE": "Golloshi et al., 2018"}]
Pool_Member_@attributes_sample_title: Progeria‐167‐DpnII‐P19‐R1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Progeria‐167‐DpnII‐P19‐R1
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