EXPERIMENT_TITLE: GSM2386379: THP-1(BglII); Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: Follow DLO Hi-C library construction protocol. Cells were double cross-linked with EGS and formaldehyde and then digested with a restriction enzyme. The digested chromatins were divided into two tubes, ligated with different 20-bp half linkers by the simultaneous digestion and ligation, and subsequently mixed for in-gel proximity ligation. The ligated DNA was purified and digested by MmeI, which released specific 80-bp DLO Hi-C DNA fragments. These DLO Hi-C DNA fragments were ligated with Illumina adapters and subjected to high-throughput sequencing
STUDY_DESCRIPTOR_STUDY_ABSTRACT: we developed a simple Digestion-Ligation-Only Hi-C (DLO Hi-C) technology to explore the 3D landscape of the genome Overall design: The DLO Hi-C library of K562 and THP-1
SAMPLE_TITLE: THP-1(BglII)
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "peripheral blood monocyte cells"}, {"TAG": "tissue", "VALUE": "peripheral blood monocyte cells"}, {"TAG": "cell line", "VALUE": "THP-1"}]
Pool_Member_@attributes_sample_title: THP-1(BglII)
RUN_SET_RUN_Pool_Member_@attributes_sample_title: THP-1(BglII)
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": null, "@attributes": {"cluster": "public", "filename": "WGC079805-TTAGGC_combined_R1.fastq.gz", "size": "7953218733", "date": "2020-04-02 16:27:52", "md5": "e4f2fe00da50f49785dd98b5623b36a1", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "WGC079805-TTAGGC_combined_R2.fastq.gz", "size": "9526994226", "date": "2020-04-02 15:42:33", "md5": "9cfc35351e98c42bd777310047c0a700", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5005052.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/005/SRR5005052.sralite.1", "size": "8021201472", "date": "2021-06-15 18:47:46", "md5": "5dc93bfc5a49ca4076ac432d3f56f173", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5005052", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5005052/SRR5005052", "size": "16553112572", "date": "2016-11-08 16:48:19", "md5": "b47d2e872081fcba76b27d952889d64a", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}]