{"lab": {"@type": ["Lab", "Item"], "correspondence": [{"contact_email": "YmVub2l0LmJydW5lYXVAZ2xhZHN0b25lLnVjc2YuZWR1", "@id": "/users/c015dffd-4ca1-4070-905f-8a04b3754b2b/", "display_title": "Benoit Bruneau"}], "display_title": "Benoit Bruneau, UCSF", "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "@id": "/labs/benoit-bruneau-lab/", "status": "current", "title": "Benoit Bruneau, UCSF", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "award": {"name": "external-award", "display_title": "EXTERNAL AWARD", "center": "External", "project": "External", "status": "current", "center_title": "External", "description": "Funding source is from outside 4DN.", "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@type": ["Award", "Item"], "@id": "/awards/external-award/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "study": "CTCF Protein Function", "status": "released", "aliases": ["4dn-dcic-lab:GSM2644947-Hi-C-auxin-2days"], "accession": "4DNES7UKQHOX", "condition": "CTCF-depleted by auxin treatment", "description": "Hi-C of CTCF-AID mouse embryonic stem cells treated with Auxin for 2 days", "study_group": "Disrupted or Atypical Cells", "date_created": "2018-11-07T21:12:56.659088+00:00", "submitted_by": {"error": "no view permissions"}, "dataset_label": "Hi-C on CTCF-AID tagged mESCs", "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2021-01-25T05:29:48.908944+00:00"}, "public_release": "2018-12-06", "replicate_exps": [{"bio_rep_no": 1, "tec_rep_no": 1, "replicate_exp": {"uuid": "9575f75f-4016-4bda-b6b9-cd23f1f02baa", "accession": "4DNEX4DOY175", "@id": "/experiments-hi-c/4DNEX4DOY175/", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "Dilution Hi-C on ES-E14TG2a with CTCF-AID with HindIII - 4DNEX4DOY175", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"bio_rep_no": 2, "tec_rep_no": 1, "replicate_exp": {"uuid": "460d89e6-d5c8-4c29-9fbe-ae18217b2e82", "accession": "4DNEXM7DHG3P", "@id": "/experiments-hi-c/4DNEXM7DHG3P/", "status": "released", "@type": ["ExperimentHiC", "Experiment", "Item"], "display_title": "Dilution Hi-C on ES-E14TG2a with CTCF-AID with HindIII - 4DNEXM7DHG3P", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "schema_version": "2", "static_content": [{"content": {"contributing_labs": [], "title": "4DNES7UKQHOX - Processed files", "uuid": "5dd9e354-ef21-4973-bfdd-63bae4b279c3", "@id": "/higlass-view-configs/5dd9e354-ef21-4973-bfdd-63bae4b279c3/", "description": "4DNES7UKQHOX (Hi-C of CTCF-AID mouse embryonic stem cells treated with Auxin for 2 days): 4DNFI5TWFPOL", "display_title": "4DNES7UKQHOX - Processed files", "lab": {"display_title": "Benoit Bruneau, UCSF", "@type": ["Lab", "Item"], "uuid": "4dfac8f5-a868-4b29-9c11-a0932130e121", "status": "current", "@id": "/labs/benoit-bruneau-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4dfac8f5-a868-4b29-9c11-a0932130e121"]}}, "@type": ["HiglassViewConfig", "UserContent", "Item"], "award": {"status": "current", "@id": "/awards/external-award/", "@type": ["Award", "Item"], "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "filetype": "HiglassViewConfig", "name": "5dd9e354-ef21-4973-bfdd-63bae4b279c3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267307e3a"]}}, "location": "tab:processed-files", "description": "auto_generated_higlass_view_config"}], "static_headers": [{"lab": {"@id": "/labs/4dn-dcic-lab/", "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "@type": ["Lab", "Item"], "status": "current", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "Dilution Hi-C\n\n
\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n
\n\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n
\n\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n
\n\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n
\n\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n
\n\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n
\n\nDilution Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2009 and it was the first genome-wide chromosome conformation capture technique. \n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. Then, the cells are lysed and a restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated in an extremely diluted solution in order to favor the ligation of the cross-linked fragments. Then, the DNA is purified and shreared. The biotinylated fragments are pulled down from the solution with streptavidin beads and the library is constructed and sequenced. Analysis of the resulting paired-end short read sequences produces a matrix that shows the number of interactions between different DNA regions.\n
\n\nAdvances in DNA sequencing depth and molecular techniques led to the development of a improved version of this technique known as in situ Hi-C that provides higher resolution, higher accuracy, and a much faster protocol. \n
\n\nSee Lieberman-aiden et al., 2009 for more details on dilution Hi-C.\n
\n