EXPERIMENT_TITLE: GSM2694179: Hi-C GM12878; Homo sapiens; Hi-C
EXPERIMENT_DESIGN_LIBRARY_DESCRIPTOR_LIBRARY_CONSTRUCTION_PROTOC: For Hi-C, about 5M cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Formaldehyde was quenched  by 0.2M glycine. Nuclear lysates were incubated with MboI. Fragment ends were filled with biotinylated nucleotides, then ligated with T4. Ligated fragments were reverse crosslinked, purified, sonicated and size selected before Illumina libraries generation. Sequencing libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina (E7645, NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
STUDY_DESCRIPTOR_STUDY_ABSTRACT: We develop a method called open chromatin enrichment and network Hi-C (OCEAN-C) for antibody-independent mapping of global open chromatin interactions. By integrating FAIRE-seq and Hi-C, OCEAN-C detects open chromatin interactions enriched by active cis-regulatory elements. We identify more than 10,000 hubs of open chromatin interactions (HOCIs) in human cells, which are mainly active promoters and enhancers bound by many DNA-binding proteins and form interaction networks crucial for gene transcription. In addition to identifying large-scale topological structures including topologically associated domains and A/B compartments, OCEAN-C can detect HOCI-mediated chromatin interactions that are strongly associated with gene expression, super-enhancers and broad H3K4me3 domains. Overall design: Analysis of open chromatin interactions and gene regulatory networks in 3 different cell types.
SAMPLE_TITLE: Hi-C GM12878
SAMPLE_SAMPLE_ATTRIBUTES_SAMPLE_ATTRIBUTE: [{"TAG": "source_name", "VALUE": "Normal"}, {"TAG": "biomaterial_provider", "VALUE": "Coriell https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM12878&Product=CC"}, {"TAG": "cell line", "VALUE": "GM12878"}, {"TAG": "tissue", "VALUE": "peripheral blood"}, {"TAG": "cell type", "VALUE": "B lymphocyte"}, {"TAG": "age", "VALUE": "No data"}, {"TAG": "disease state", "VALUE": "Normal"}, {"TAG": "gender", "VALUE": "female"}]
Pool_Member_@attributes_sample_title: Hi-C GM12878
RUN_SET_RUN_Pool_Member_@attributes_sample_title: Hi-C GM12878
RUN_SET_RUN_SRAFiles_SRAFile: [{"Alternatives": [null, null, null], "@attributes": {"cluster": "public", "filename": "SRR5807395.sralite", "url": "https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos5/sra-pub-zq-14/SRR005/807/SRR5807395.sralite.1", "size": "15363908668", "date": "2021-06-16 03:59:32", "md5": "c7c65049d6d7618a994f8c0c99ffe3d4", "version": "1", "semantic_name": "SRA Lite", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "SRR5807395", "url": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR5807395/SRR5807395", "size": "24571351800", "date": "2017-07-05 19:53:11", "md5": "ba12f03f3c34a8121a60048a0d8186e0", "version": "1", "semantic_name": "SRA Normalized", "supertype": "Primary ETL", "sratoolkit": "1"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM12878_Hi-C_R2.fq.gz", "size": "17605095673", "date": "2020-03-24 04:12:57", "md5": "53129b63b6d4e44561d2c527df2d4c2f", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}, {"Alternatives": null, "@attributes": {"cluster": "public", "filename": "GM12878_Hi-C_R1.fq.gz", "size": "15409288404", "date": "2020-03-24 04:12:57", "md5": "acdc039a674db22b24fb0202682782dc", "version": "1", "semantic_name": "fastq", "supertype": "Original", "sratoolkit": "0"}}]