EXPERIMENT_TITLE: 16hr-digest_6hr-ligate
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: iconHi-C
STUDY_DESCRIPTOR_STUDY_ABSTRACT: This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding, by an academic third party. We release a customized "inexpensive and controllable Hi-C (iconHi-C)" protocol in which the optimization factors revealed by our benchmarking have been incorporated, as well as the resultant chromosome-scale genome assembly of the Chinese softshell turtle Pelodiscus sinensis.
SAMPLE_TITLE: Human GM12878
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "sample_name", "VALUE": "GM12878"}, {"TAG": "biomaterial_provider", "VALUE": "Coriell Cell Repositories"}, {"TAG": "collection_date", "VALUE": "2017-03-07"}, {"TAG": "env_broad_scale", "VALUE": "not applicable"}, {"TAG": "env_local_scale", "VALUE": "not applicable"}, {"TAG": "env_medium", "VALUE": "not applicable"}, {"TAG": "estimated_size", "VALUE": "3.23Gbp"}, {"TAG": "geo_loc_name", "VALUE": "not applicable"}, {"TAG": "isol_growth_condt", "VALUE": "not applicable"}, {"TAG": "lat_lon", "VALUE": "not applicable"}, {"TAG": "num_replicons", "VALUE": "1"}, {"TAG": "ploidy", "VALUE": "diploid"}, {"TAG": "project_name", "VALUE": "Multifaceted Hi-C benchmarking for chromosome-scale genome scaffolding"}, {"TAG": "propagation", "VALUE": "sexual"}, {"TAG": "cultivar", "VALUE": "missing"}, {"TAG": "ecotype", "VALUE": "missing"}, {"TAG": "isolate", "VALUE": "missing"}, {"TAG": "strain", "VALUE": "missing"}, {"TAG": "BioSampleModel", "VALUE": "MIGS.eu"}]
Pool_Member_@attributes_sample_title: Human GM12878
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Human GM12878
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "DRR191013", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/DRR191013/DRR191013", "size": "826230782", "date": "2019-10-04 16:23:58", "md5": "0148d85e17940ab6a4c8045ee6d2e489", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "DRR191013.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-16/DRR000/191/DRR191013.sralite.1", "size": "419039998", "date": "2020-06-19 22:21:14", "md5": "b450991ef248edec005f1bc17ef902fc", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}]