EXPERIMENT_TITLE: GSM8123836: knee chondrocytes rep5; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Cartilage samples were cut into tiny pieces and transferred into a Falcon tube, washed with PBS twice and then digested in DMEM with 3mg/mL Collagenase 1A (Sigma, #C9891) on a 37°C shaker overnight. Tissue suspensions were passed through a 70 µm cell strainer and single chondrocytes were collected. Cells were washed with PBS and split into aliquots. Approximately 2 million primary chondrocytes were crosslinked in 2% formaldehyde for 10 minutes at room temperature and the reaction was then quenched using a solution of 0.125M glycine (Sigma, #50046) + 3% BSA (Sigma, #A9647). Samples were then washed in PBS, snap frozen on dry ice and transferred to -80°C for long-term storage. One million chondrocyte cells were used for library preparation using the two-restriction enzyme Arima Hi-C kit (Arima Genomics) and the KAPA HyperPrep kit (Roche #KK8504) following manufacturer's protocols and using Illumina TruSeq dual indexes.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: Osteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organization in 3D space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner. Here, we generate the first whole genome chromosome conformation analysis (Hi-C) map of primary osteoarthritis chondrocytes. Overall design: Human knee cartilage samples were collected during routine joint replacement surgery. Healthy cartilage was defined according to the International Cartilage Repair Society macroscopic grading system (Grade 0-1).
SAMPLE_TITLE: knee chondrocytes rep5
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "primary chondrocytes form the knee"}, {"TAG": "tissue", "VALUE": "primary chondrocytes form the knee"}, {"TAG": "geo_loc_name", "VALUE": "missing"}, {"TAG": "collection_date", "VALUE": "missing"}]
Pool_Member_@attributes_sample_title: knee chondrocytes rep5
RUN_SET_RUN_Pool_Member_@attributes_sample_title: knee chondrocytes rep5
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