EXPERIMENT_TITLE: GSM8476291: A375-Clone3-ITGB4neg-R1; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: The first biological replicate of ITGB4 sorted cells was processed with the protocol described in (Golloshi et al., 2018). Briefly, 10 million cells were crosslinked with 1% formaldehyde for 10 min. Crosslinked cells were then suspended in lysis buffer to permeabilize the cell membrane and were dounce homogenized. Chromatin was then digested in-nucleus overnight using the DpnII restriction enzyme. Digested ends were filled in with biotin-dATP, and the blunt ends of interacting fragments were ligated together. DNA was then purified by phenol-chloroform extraction. For library preparation, the NEBNext Ultra II DNA Library prep kit (NEB) was used for libraries with size ranges from 200-400bp. End Prep, Adaptor Ligation, and PCR amplification reactions were carried out on bead-bound DNA libraries.  All other Hi-C experiments were performed using the Arima‐HiC+ Kit from Arima Genomics following the protocol for Mammalian Cell Lines (A160134 v01) and preparing the libraries using Arima recommendations for the NEBNext Ultra II DNA library prep kit (protocol version A16041v01). 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: Metastatic cancer cells traverse tight junctions that exert forces on their nucleus and the genomic contents within. Cancerous tumors are highly heterogeneous and not all cells within them can achieve such a feat. Here, we investigated what initial genome architecture characteristics favor the constricted migratory ability of cancer cells and which arise only after passage through multiple constrictions. We identified a cell surface protein (ITGB4) whose expression correlates with increased initial constricted migration ability in human melanoma A375 cells. Sorting out this subpopulation allowed us to identify cellular and nuclear features that pre-exist and favor migration, as well as alterations that only appear after cells have passed through constrictions.  We identified specific genomic regions that experienced altered genome spatial compartment profiles only after constricted migration. Our study reveals 3D genome structure contributions to both selection and induction mechanisms of cell fate change during cancer metastasis. Overall design: A375 cells from either the original cell line population (Parental) or a population grown from a single cell (Clone3) were FACS sorted according to expression of Integrin Beta 4 (ITGB4).  Cells were then allowed to migrate through 5 rounds of constricted migration.  Genome structure was characterized by Hi-C across all populations and migration conditions.
SAMPLE_TITLE: A375-Clone3-ITGB4neg-R1
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Melanoma (A375)"}, {"TAG": "cell line", "VALUE": "Melanoma (A375)"}, {"TAG": "genotype", "VALUE": "Clonal population, No ITGB4 expression"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: A375-Clone3-ITGB4neg-R1
RUN_SET_RUN_Pool_Member_@attributes_sample_title: A375-Clone3-ITGB4neg-R1
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