{"lab": {"title": "Benjamin Rowland, NKI", "status": "current", "@type": ["Lab", "Item"], "uuid": "6e1ac73e-bdb7-4995-b003-2c31f538049a", "display_title": "Benjamin Rowland, NKI", "@id": "/labs/benjamin-rowland-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.6e1ac73e-bdb7-4995-b003-2c31f538049a"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "project": "External", "center": "External", "description": "Funding source is from outside 4DN.", "status": "current", "@type": ["Award", "Item"], "center_title": "External", "name": "external-award", "@id": "/awards/external-award/", "display_title": "EXTERNAL AWARD", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"uuid": "393f7843-7a46-401d-84a0-67d57aa8c10b", "file_size": 3912813790, "href": "/files-fastq/4DNFIOS4QDI1/@@download/4DNFIOS4QDI1.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIOS4QDI1", "paired_end": "1", "@id": "/files-fastq/4DNFIOS4QDI1/", "dbxrefs": ["SRA:SRR5266586"], "upload_key": "393f7843-7a46-401d-84a0-67d57aa8c10b/4DNFIOS4QDI1.fastq.gz", "display_title": "4DNFIOS4QDI1.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "display_title": "4DNFIY9A98UL.fastq.gz", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "uuid": "44895505-51b9-49e0-8a1f-bf8db5c86b00", "file_type": "reads", "@id": "/files-fastq/4DNFIY9A98UL/", "accession": "4DNFIY9A98UL", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIOS4QDI1/fastqc_report.html", "Sequence length": "100", "status": "released", "uuid": "b7c6b71e-86c9-4e64-8cde-ab4dea92c008", "Total Sequences": 56494110, "display_title": "QualityMetricFastqc from 2018-11-17", "@id": "/quality-metrics-fastqc/b7c6b71e-86c9-4e64-8cde-ab4dea92c008/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5266586", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5266586"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "44895505-51b9-49e0-8a1f-bf8db5c86b00", "file_size": 3778504227, "href": "/files-fastq/4DNFIY9A98UL/@@download/4DNFIY9A98UL.fastq.gz", "file_type_detailed": "reads (fastq)", "file_type": "reads", "file_classification": "raw file", "accession": "4DNFIY9A98UL", "paired_end": "2", "@id": "/files-fastq/4DNFIY9A98UL/", "dbxrefs": ["SRA:SRR5266586"], "upload_key": "44895505-51b9-49e0-8a1f-bf8db5c86b00/4DNFIY9A98UL.fastq.gz", "display_title": "4DNFIY9A98UL.fastq.gz", "status": "released", "@type": ["FileFastq", "File", "Item"], "file_format": {"file_format": "fastq", "status": "released", "@id": "/file-formats/fastq/", "@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "display_title": "4DNFIOS4QDI1.fastq.gz", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "uuid": "393f7843-7a46-401d-84a0-67d57aa8c10b", "file_type": "reads", "@id": "/files-fastq/4DNFIOS4QDI1/", "accession": "4DNFIOS4QDI1", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "quality_metric": {"url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIY9A98UL/fastqc_report.html", "Sequence length": "98", "status": "released", "uuid": "e701a03c-ce12-4ac3-aba0-2f77d7607f35", "Total Sequences": 56494110, "display_title": "QualityMetricFastqc from 2018-11-17", "@id": "/quality-metrics-fastqc/e701a03c-ce12-4ac3-aba0-2f77d7607f35/", "overall_quality_status": "PASS", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5266586", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5266586"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2494292"], "dbxrefs": ["GEO:GSM2494292"], "protocol": {"@id": "/protocols/692f7810-e44b-4c1b-9e1d-a79cd9998ef2/", "status": "released", "display_title": "InsituHiC.pdf", "uuid": "692f7810-e44b-4c1b-9e1d-a79cd9998ef2", "@type": ["Protocol", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXV5HTNBS", "biosample": {"status": "released", "@id": "/biosamples/4DNBSOLYNBQA/", "display_title": "4DNBSOLYNBQA", "accession": "4DNBSOLYNBQA", "@type": ["Biosample", "Item"], "biosample_type": "immortalized cells", "biosource_summary": "HAP-1", "uuid": "44ab68ba-b17d-4713-ad88-e9c5a192a620", "treatments_summary": "None", "modifications_summary": "Crispr deletion of SCC4", "biosource": [{"lab": {"uuid": "5771d772-1d10-43ea-bec1-0ea8c5a58503", "@type": ["Lab", "Item"], "display_title": "Erez Lieberman Aiden, BCM", "status": "current", "@id": "/labs/erez-liebermanaiden-lab/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.5771d772-1d10-43ea-bec1-0ea8c5a58503"]}}, "url": "https://www.horizondiscovery.com/cell-lines/all-products/about-x-man-cell-lines/hap1-cells", "award": {"uuid": "36a06537-7831-494d-b10d-3e9fea931021", "@type": ["Award", "Item"], "status": "current", "@id": "/awards/OD008540-01/", "display_title": "EXPLORING HOW THE GENOME FOLDS THROUGH PROXIMITY LIGATION AND SEQUENCING", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"term_id": "CL:0000081", "uuid": "0d64fbe2-ed5c-43cd-a30d-d9f0320d27ed", "status": "released", "term_name": "blood cell", "@type": ["OntologyTerm", "Item"], "@id": "/ontology-terms/CL:0000081/", "display_title": "blood cell", "slim_terms": [{"uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "display_title": "cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "preferred_name": "blood cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["dcic:hap1cells"], "accession": "4DNSRNIAESOK", "cell_line": {"slim_terms": [{"display_title": "cell", "@id": "/ontology-terms/CL:0000000/", "status": "released", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"display_title": "cell", "@id": "/ontology-terms/GO:0005623/", "status": "current", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "@id": "/ontology-terms/EFO:0007598/", "uuid": "57d18eec-d662-4bf7-8000-047de03ad84a", "term_name": "HAP-1", "term_id": "EFO:0007598", "@type": ["OntologyTerm", "Item"], "display_title": "HAP-1", "synonyms": ["HAP1"], "preferred_name": "HAP-1", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "uuid": "6e37c213-33dd-4aff-aedb-b466a4b2aa45", "@id": "/individuals-human/4DNINGLJ7A6Z/", "protected_data": false, "display_title": "4DNINGLJ7A6Z", "@type": ["IndividualHuman", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "references": [], "description": "HAP-1 a near haploid cell line", "date_created": "2017-04-10T01:05:47.201162+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2019-06-05T14:29:58.101324+00:00"}, "modifications": [], "biosource_type": "immortalized cell line", "cell_line_tier": "Unclassified", "public_release": "2017-04-10", "schema_version": "2", "project_release": "2017-04-10", "biosource_vendor": {"display_title": "Horizon Genomics", "status": "released", "@type": ["Vendor", "Item"], "uuid": "1fd06d82-b232-46ec-91f7-f18593f43e9d", "@id": "/vendors/horizon-genomics/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "alternate_accessions": [], "@id": "/biosources/4DNSRNIAESOK/", "@type": ["Biosource", "Item"], "uuid": "18fc203e-0b65-43b7-8373-0c8fdf5eff57", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "HAP-1 - 4DNSRNIAESOK", "external_references": [], "biosource_name": "HAP-1", "biosource_category": ["Tier 2"], "organism": {"display_title": "H. sapiens", "name": "human", "@id": "/organisms/9606/", "@type": ["Organism", "Item"], "status": "released", "uuid": "7745b647-ff15-4ff3-9ced-b897d4e2983c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "badges": [{"messages": ["Biosample missing Cell Culture Details", "HAP-1 biosample missing ploidy authentication"], "badge": {"@id": "/badges/biosample-metadata-incomplete/", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group.", "status": "released", "display_title": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@type": ["Badge", "Item"], "badge_icon": "/static/img/badges/biosample-icon.svg", "title": "Biosample Metadata Incomplete", "warning": "Biosample Metadata Incomplete", "badge_classification": "Warning", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "modifications": [{"display_title": "Crispr deletion of SCC4", "modification_type": "Crispr", "@id": "/modifications/98b75b88-14b3-46b5-a8a6-419465f655fd/", "@type": ["Modification", "Item"], "genomic_change": "disruption", "status": "released", "uuid": "98b75b88-14b3-46b5-a8a6-419465f655fd", "description": "CRISPRs targeting SCC4 (5\u2019-CACCGTACGGGCCTCGATGCGCTG-3\u2019) were cloned into px330 (Addgene plasmid #42230). \u2206SCC4 HAP1 clones were generated by insertion of a Puromycin cassette as previously described (Blomen et al., 2015).", "override_modification_name": "Crispr deletion of SCC4", "target_of_mod": [{"status": "released", "display_title": "SCC4 gene", "@id": "/bio-features/969062b2-2787-4804-be5c-7b01249d9b81/", "relevant_genes": [{"@id": "/genes/23383/", "@type": ["Gene", "Item"], "display_title": "SCC4", "status": "released", "uuid": "3e0348e2-c4d5-4bd8-aac4-0512842d0dbd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "organism_name": "human", "feature_type": {"uuid": "0231da78-1adc-4b8a-89b9-4f91908412a3", "@type": ["OntologyTerm", "Item"], "status": "released", "display_title": "gene", "@id": "/ontology-terms/SO:0000704/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "uuid": "969062b2-2787-4804-be5c-7b01249d9b81", "@type": ["BioFeature", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "SCC4KO-A Hi-C", "sop_mapping": {"has_sop": "No"}, "date_created": "2018-10-17T20:57:07.753496+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-07-19T13:22:11.014926+00:00"}, "public_release": "2018-12-06", "schema_version": "2", "tagging_method": "bio-dATP", "experiment_type": {"display_title": "in situ Hi-C", "title": "in situ Hi-C", "@type": ["ExperimentType", "Item"], "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "experiment_category": "Sequencing", "status": "released", "assay_subclass_short": "Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"@id": "/files-processed/4DNFI2Z869FJ/", "file_size": 11824315164, "display_title": "4DNFI2Z869FJ.bam", "status": "released", "href": "/files-processed/4DNFI2Z869FJ/@@download/4DNFI2Z869FJ.bam", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/3cfb95ea-0050-4095-9b9a-fd009a0a6d25/4DNFI2Z869FJ.bam", "@type": ["FileProcessed", "File", "Item"], "uuid": "3cfb95ea-0050-4095-9b9a-fd009a0a6d25", "accession": "4DNFI2Z869FJ", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "bam", "display_title": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "alignments", "file_classification": "processed file", "file_type_detailed": "alignments (bam)", "upload_key": "3cfb95ea-0050-4095-9b9a-fd009a0a6d25/4DNFI2Z869FJ.bam", "quality_metric": {"@id": "/quality-metrics-bamqc/447ad7e0-c958-4fe5-b798-f5b26bf49a99/", "status": "released", "display_title": "QualityMetricBamqc from 2019-12-13", "overall_quality_status": "PASS", "uuid": "447ad7e0-c958-4fe5-b798-f5b26bf49a99", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "56494110", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "6.502", "tooltip": "Percent of total reads (=3.67m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "10.886", "tooltip": "Percent of total reads (=6.15m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "0.61", "tooltip": "Percent of total reads (=0.34m)", "numberType": "percent"}, {"title": "Walks", "value": "7.788", "tooltip": "Percent of total reads (=4.4m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.199", "tooltip": "Percent of total reads (=0.11m)", "numberType": "percent"}]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Benjamin Rowland, NKI", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "SCC4 knock out", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/files-processed/4DNFIVNCTHHT/", "file_size": 859120911, "display_title": "4DNFIVNCTHHT.pairs.gz", "status": "released", "href": "/files-processed/4DNFIVNCTHHT/@@download/4DNFIVNCTHHT.pairs.gz", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/25b3b2d6-446b-4f95-84b3-966bf8044311/4DNFIVNCTHHT.pairs.gz", "@type": ["FileProcessed", "File", "Item"], "uuid": "25b3b2d6-446b-4f95-84b3-966bf8044311", "accession": "4DNFIVNCTHHT", "file_format": {"uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "@type": ["FileFormat", "Item"], "status": "released", "file_format": "pairs", "display_title": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_type": "contact list-replicate", "file_classification": "processed file", "file_type_detailed": "contact list-replicate (pairs)", "upload_key": "25b3b2d6-446b-4f95-84b3-966bf8044311/4DNFIVNCTHHT.pairs.gz", "quality_metric": {"@id": "/quality-metrics-pairsqc/c7d15131-f8f7-4c9b-b187-4d2798f24bf9/", "status": "released", "display_title": "QualityMetricPairsqc from 2018-12-05", "overall_quality_status": "PASS", "uuid": "c7d15131-f8f7-4c9b-b187-4d2798f24bf9", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIVNCTHHT/pairsqc_report.html", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 41926781, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "41926781", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "55.305", "tooltip": "Percent of filtered reads (=23.19m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.681", "tooltip": "Percent of filtered reads (=9.09m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "23.014", "tooltip": "Percent of filtered reads (=9.65m)", "numberType": "percent"}]}, "external_references": [], "track_and_facet_info": {"experimental_lab": "Benjamin Rowland, NKI", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "SCC4 knock out", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "project_release": "2018-12-06", "digestion_enzyme": {"display_title": "MboI", "@type": ["Enzyme", "Item"], "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "@id": "/enzymes/MboI/", "status": "released", "name": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "biosample_quantity": 10000000.0, "crosslinking_method": "2% Formaldehyde", "fragmentation_method": "sonication", "other_processed_files": [{"type": "preliminary", "files": [{"display_title": "4DNFIWJPOV2W.bam", "file_type": "alignments", "@type": ["FileProcessed", "File", "Item"], "uuid": "fce17482-693e-4d1e-9ae2-287440cdc2e8", "file_type_detailed": "alignments (bam)", "status": "released", "href": "/files-processed/4DNFIWJPOV2W/@@download/4DNFIWJPOV2W.bam", "@id": "/files-processed/4DNFIWJPOV2W/", "genome_assembly": "GRCh38", "file_size": 11804804621, "accession": "4DNFIWJPOV2W", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/fce17482-693e-4d1e-9ae2-287440cdc2e8/4DNFIWJPOV2W.bam", "track_and_facet_info": {"experimental_lab": "Benjamin Rowland, NKI", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "MboI", "dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "SCC4 knock out", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "file_format": "bam", "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-07T23:22:16.828888+00:00"}}, {"display_title": "4DNFIWXIYUEL.pairs.gz", "file_type": "contact list-replicate", "@type": ["FileProcessed", "File", "Item"], "uuid": "f409fe5d-547f-4693-b87a-e3b8d1853893", "file_type_detailed": "contact list-replicate (pairs)", "status": "released", "href": "/files-processed/4DNFIWXIYUEL/@@download/4DNFIWXIYUEL.pairs.gz", "@id": "/files-processed/4DNFIWXIYUEL/", "genome_assembly": "GRCh38", "file_size": 871719784, "accession": "4DNFIWXIYUEL", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/f409fe5d-547f-4693-b87a-e3b8d1853893/4DNFIWXIYUEL.pairs.gz", "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "status": "released", "overall_quality_status": "PASS", "display_title": "QualityMetricPairsqc from 2024-07-08", "uuid": "c027d782-b6e3-42b4-82ea-dbb3caa2fe3b", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIWXIYUEL/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/c027d782-b6e3-42b4-82ea-dbb3caa2fe3b/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "44989638", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "55.211", "tooltip": "Percent of filtered reads (=24.84m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "21.049", "tooltip": "Percent of filtered reads (=9.47m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "23.74", "tooltip": "Percent of filtered reads (=10.68m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "Benjamin Rowland, NKI", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "MboI", "dataset": "Hi-C on HAP-1 +/- WAPL or SCC4 KO", "condition": "SCC4 knock out", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "HAP-1", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-07T23:20:51.706391+00:00"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "cells", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-hi-c/4DNEXV5HTNBS/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "61056209-cc2d-44a9-8b9d-cd0b79d11315", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on HAP-1 with MboI - 4DNEXV5HTNBS", "external_references": [{"ref": "GEO:GSM2494292", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2494292"}], "experiment_sets": [{"experimentset_type": "replicate", "status": "released", "@id": "/experiment-set-replicates/4DNESNLXBFMY/", "accession": "4DNESNLXBFMY", "uuid": "9094ec5b-1e2d-4c2c-bb38-e6e5b0222ce9", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESNLXBFMY", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"authors": ["Haarhuis JHI", "van der Weide RH", "Blomen VA", "Yanez-Cuna JO", "Amendola M", "van Ruiten MS", "Krijger PHL", "Teunissen H", "Medema RH", "van Steensel B", "Brummelkamp TR", "de Wit E", "Rowland BD"], "short_attribution": "Haarhuis JHI et al. (2017)", "status": "current", "uuid": "4b1d9cd4-c791-40c6-8b81-8a987f696f32", "@type": ["Publication", "Item"], "ID": "PMID:28475897", "display_title": "Haarhuis JHI et al. (2017) PMID:28475897", "abstract": "The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can  be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin's DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.", "title": "The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.", "journal": "Cell", "@id": "/publications/4b1d9cd4-c791-40c6-8b81-8a987f696f32/", "date_published": "2017-05-04", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"abstract": "The spatial organization of chromosomes influences many nuclear processes including gene expression. The cohesin complex shapes the 3D genome by looping together CTCF sites along chromosomes. We show here that chromatin loop size can  be increased and that the duration with which cohesin embraces DNA determines the degree to which loops are enlarged. Cohesin's DNA release factor WAPL restricts this loop extension and also prevents looping between incorrectly oriented CTCF sites. We reveal that the SCC2/SCC4 complex promotes the extension of chromatin loops and the formation of topologically associated domains (TADs). Our data support the model that cohesin structures chromosomes through the processive enlargement of loops and that TADs reflect polyclonal collections of loops in the making. Finally, we find that whereas cohesin promotes chromosomal looping, it rather limits nuclear compartmentalization. We conclude that the balanced activity of SCC2/SCC4 and WAPL enables cohesin to correctly structure chromosomes.", "@type": ["Publication", "Item"], "ID": "PMID:28475897", "authors": ["Haarhuis JHI", "van der Weide RH", "Blomen VA", "Yanez-Cuna JO", "Amendola M", "van Ruiten MS", "Krijger PHL", "Teunissen H", "Medema RH", "van Steensel B", "Brummelkamp TR", "de Wit E", "Rowland BD"], "@id": "/publications/4b1d9cd4-c791-40c6-8b81-8a987f696f32/", "short_attribution": "Haarhuis JHI et al. (2017)", "display_title": "Haarhuis JHI et al. (2017) PMID:28475897", "title": "The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension.", "status": "current", "uuid": "4b1d9cd4-c791-40c6-8b81-8a987f696f32", "date_published": "2017-05-04", "journal": "Cell", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on HAP-1 with MboI", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSOLYNBQA/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details", "HAP-1 biosample missing ploidy authentication"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}