![](\"https://s3.amazonaws.com/4dn-dcic-public/static-pages/InfoBoxes/IsHC_fig1.png\"/)
\n \n Image source: Rao et al., 2014, Figure 1A\n
\n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter 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 and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a 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\nSee Rao et al., 2014 for more details.\n
\n\n\n \n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter 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 and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a 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\nSee Rao et al., 2014 for more details.\n
\n\n\n \n In situ Hi-C is a method to detect and quantify the pairwise interactions between chromosome regions across the entire genome. It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed in situ inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n
\n\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter 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 and the DNA is purified and sheared. The biotinylated fragments are pulled down from the solution with streptavidin beads and a 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\nSee Rao et al., 2014 for more details.\n
\n\n\n Some annotated bam and pairs files generated in this Experiment Set may contain distinct reads that share the same identifier. This was caused by merging fastq files with integer identifiers (eg. @1, @2) during processing.
"}], "processed_files": [{"file_type": "contact list-combined", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/09697b2d-4b8f-47a2-8dd5-d8da37eabab9/4DNFIAS9CGMR.pairs.gz", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIAS9CGMR/", "accession": "4DNFIAS9CGMR", "file_classification": "processed file", "file_format": {"status": "released", "@id": "/file-formats/pairs/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "pairs", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["WARNING: some distinct reads in this file may share the same identifier because the file was generated after merging fastq files with integer identifiers (eg. @1, @2) during processing."], "display_title": "4DNFIAS9CGMR.pairs.gz", "upload_key": "09697b2d-4b8f-47a2-8dd5-d8da37eabab9/4DNFIAS9CGMR.pairs.gz", "uuid": "09697b2d-4b8f-47a2-8dd5-d8da37eabab9", "file_type_detailed": "contact list-combined (pairs)", "href": "/files-processed/4DNFIAS9CGMR/@@download/4DNFIAS9CGMR.pairs.gz", "status": "released", "md5sum": "f2e58dbf1715dfd424b5815a2182eadd", "file_size": 1268767424, "quality_metric": {"@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "display_title": "QualityMetricPairsqc from 2020-01-24", "uuid": "e684d661-01f6-4d61-8f1a-f1211a033852", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIAS9CGMR/pairsqc_report.html", "status": "released", "@id": "/quality-metrics-pairsqc/e684d661-01f6-4d61-8f1a-f1211a033852/", "Total reads": 86910877, "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "86910877", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "24.886", "tooltip": "Percent of filtered reads (=21.63m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "37.971", "tooltip": "Percent of filtered reads (=33.0m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "37.143", "tooltip": "Percent of filtered reads (=32.28m)", "numberType": "percent"}]}, "lab": {"status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "display_title": "Wei Xie, TSINGHUA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "extra_files": [{"file_size": 8748965, "href": "/files-processed/4DNFIAS9CGMR/@@download/4DNFIAS9CGMR.pairs.gz.px2", "md5sum": "bfa489bf38f7de4063a89ea5475b2b0b", "file_format": {"file_format": "pairs_px2", "display_title": "pairs_px2", "status": "released", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs_px2/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [], "last_modified": {"date_modified": "2021-04-06T20:18:56.805417+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "experimental_lab": "Wei Xie, TSINGHUA", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}}, {"file_type": "contact matrix", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/27f54fcb-54fe-41a4-b25a-2f8944c89044/4DNFIN8F14CS.hic", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIN8F14CS/", "accession": "4DNFIN8F14CS", "file_classification": "processed file", "file_format": {"status": "released", "@id": "/file-formats/hic/", "uuid": "d13d11cf-218e-4f61-bbf0-91f226248b2c", "display_title": "hic", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIN8F14CS.hic", "upload_key": "27f54fcb-54fe-41a4-b25a-2f8944c89044/4DNFIN8F14CS.hic", "uuid": "27f54fcb-54fe-41a4-b25a-2f8944c89044", "file_type_detailed": "contact matrix (hic)", "href": "/files-processed/4DNFIN8F14CS/@@download/4DNFIN8F14CS.hic", "status": "released", "md5sum": "c3969021a5d09aea06c4f84de9480981", "file_size": 1427005824, "lab": {"status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "display_title": "Wei Xie, TSINGHUA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "external_references": [], "last_modified": {"date_modified": "2020-04-14T02:40:09.054611+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "experimental_lab": "Wei Xie, TSINGHUA", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}}, {"file_type": "contact matrix", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/d1202a64-161e-4022-a6ac-a54e4c92d71f/4DNFIX3TBE4Y.mcool", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIX3TBE4Y/", "accession": "4DNFIX3TBE4Y", "higlass_uid": "19e6bbc6-4285-4d62-b25d-7680de34a947", "file_classification": "processed file", "file_format": {"status": "released", "@id": "/file-formats/mcool/", "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "display_title": "mcool", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "notes_to_tsv": ["WARNING - Due to a bug in the version of cooler (0.8.3) used in the current 4DN standard Hi-C processing pipeline some pixels may occur mulitple times at a single resolution with different counts being reported for each occurence. This duplication does not affect the higlass display of these files, howevver, downstream analyses using this file may encounter issues due to this pixel duplication. The counts from the duplicate pixels can be aggregated to determine the correct count value at that location. If this issue is problematic for your needs you should consider regenerating the matrices from the merged pairs file of the associated dataset using a more recent version of cooler. We are working to update the pipeline but do not yet have a predicted date for when this issue will be resolved."], "display_title": "4DNFIX3TBE4Y.mcool", "upload_key": "d1202a64-161e-4022-a6ac-a54e4c92d71f/4DNFIX3TBE4Y.mcool", "uuid": "d1202a64-161e-4022-a6ac-a54e4c92d71f", "file_type_detailed": "contact matrix (mcool)", "href": "/files-processed/4DNFIX3TBE4Y/@@download/4DNFIX3TBE4Y.mcool", "status": "released", "md5sum": "b55bd176bbf5fa60e335cba5b3d18689", "file_size": 854230443, "quality_metric": {"@type": ["QualityMetricMcool", "QualityMetric", "Item"], "display_title": "QualityMetricMcool from 2021-05-21", "uuid": "4cec86be-4812-4300-bc9a-84f8d91e56a7", "status": "released", "@id": "/quality-metrics-mcool/4cec86be-4812-4300-bc9a-84f8d91e56a7/", "overall_quality_status": "PASS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Failed Balancing", "value": "None", "tooltip": "Resolutions where balancing failed", "numberType": "string"}]}, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "@id": "/higlass-view-configs/95c91132-387c-4350-bf5a-b2a3b1f3f763/", "uuid": "95c91132-387c-4350-bf5a-b2a3b1f3f763", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIX3TBE4Y - contact matrix for sperm in situ Hi-C MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "display_title": "Wei Xie, TSINGHUA", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "external_references": [], "last_modified": {"date_modified": "2023-08-25T17:50:40.885696+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "experimental_lab": "Wei Xie, TSINGHUA", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA", "track_title": "contact matrix for sperm in situ Hi-C MboI"}}, {"file_type": "compartments", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/1996430f-5198-41f7-ac99-417f2cba2c5e/4DNFIR4F63SC.bw", "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "@id": "/files-processed/4DNFIR4F63SC/", "accession": "4DNFIR4F63SC", "higlass_uid": "3b8312ed-0120-459e-aa56-ee98e2a77691", "file_classification": "processed file", "file_format": {"status": "released", "@id": "/file-formats/bw/", "uuid": "d1311111-218e-4f61-aaf0-91f226248b2c", "display_title": "bw", "@type": ["FileFormat", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "display_title": "4DNFIR4F63SC.bw", "upload_key": "1996430f-5198-41f7-ac99-417f2cba2c5e/4DNFIR4F63SC.bw", "uuid": "1996430f-5198-41f7-ac99-417f2cba2c5e", "file_type_detailed": "compartments (bw)", "href": "/files-processed/4DNFIR4F63SC/@@download/4DNFIR4F63SC.bw", "status": "released", "md5sum": "e78fd31186bc6a97b1391450d7e39531", "file_size": 193718, "static_content": [{"description": "auto_generated_higlass_view_config", "location": "tab:higlass", "content": {"status": "released", "@id": "/higlass-view-configs/abd412f5-e440-4932-9b93-4f28a4138ee8/", "uuid": "abd412f5-e440-4932-9b93-4f28a4138ee8", "@type": ["HiglassViewConfig", "UserContent", "Item"], "display_title": "4DNFIR4F63SC - compartments for sperm in situ Hi-C MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "lab": {"status": "current", "@id": "/labs/4dn-dcic-lab/", "name": "4dn-dcic-lab", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "display_title": "4DN DCIC, HMS", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "contributing_labs": [{"display_title": "Wei Xie, TSINGHUA", "@type": ["Lab", "Item"], "@id": "/labs/wei-xie-lab/", "status": "current", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "name": "wei-xie-lab", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}], "external_references": [], "last_modified": {"date_modified": "2021-03-28T14:09:18.920054+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "track_and_facet_info": {"dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "experimental_lab": "Wei Xie, TSINGHUA", "replicate_info": "merged replicates", "experiment_bucket": "processed file", "experiment_type": "in situ Hi-C", "assay_info": "MboI", "biosource_name": "sperm", "lab_name": "4DN DCIC, HMS", "track_title": "compartments for sperm in situ Hi-C MboI"}}], "project_release": "2020-02-07", "experiments_in_set": [{"display_title": "in situ Hi-C on sperm with MboI - 4DNEXZK3P2RC", "@id": "/experiments-hi-c/4DNEXZK3P2RC/", "dbxrefs": ["GEO:GSM2434086"], "files": [{"file_size": 7258409644, "file_type": "reads", "uuid": "4665eb25-3729-446d-af3c-aab94350ed32", "dbxrefs": ["SRA:SRR5122738"], "href": "/files-fastq/4DNFIJSJTQWR/@@download/4DNFIJSJTQWR.fastq.gz", "paired_end": "1", "accession": "4DNFIJSJTQWR", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/4665eb25-3729-446d-af3c-aab94350ed32/4DNFIJSJTQWR.fastq.gz", "display_title": "4DNFIJSJTQWR.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "4665eb25-3729-446d-af3c-aab94350ed32/4DNFIJSJTQWR.fastq.gz", "md5sum": "51cdfe763f4a169eff3f97a45a11e3ff", "@id": "/files-fastq/4DNFIJSJTQWR/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 91344505, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "896bb40f-6b37-4f0c-a6fb-6d9d02811492", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/896bb40f-6b37-4f0c-a6fb-6d9d02811492/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJSJTQWR/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIMG5GS2I.fastq.gz", "accession": "4DNFIMG5GS2I", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIMG5GS2I/", "paired_end": "2", "status": "released", "file_type": "reads", "uuid": "de34add4-672f-4f2b-b772-1fd0989f5303", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122738", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122738"}]}, {"file_size": 8315208607, "file_type": "reads", "uuid": "de34add4-672f-4f2b-b772-1fd0989f5303", "dbxrefs": ["SRA:SRR5122738"], "href": "/files-fastq/4DNFIMG5GS2I/@@download/4DNFIMG5GS2I.fastq.gz", "paired_end": "2", "accession": "4DNFIMG5GS2I", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/de34add4-672f-4f2b-b772-1fd0989f5303/4DNFIMG5GS2I.fastq.gz", "display_title": "4DNFIMG5GS2I.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "de34add4-672f-4f2b-b772-1fd0989f5303/4DNFIMG5GS2I.fastq.gz", "md5sum": "715d4e58c5163fc41f418dc2a8d459e2", "@id": "/files-fastq/4DNFIMG5GS2I/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 91344505, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "0f5e068a-44a1-4cba-a843-10f8e6ec629e", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/0f5e068a-44a1-4cba-a843-10f8e6ec629e/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMG5GS2I/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIJSJTQWR.fastq.gz", "accession": "4DNFIJSJTQWR", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIJSJTQWR/", "paired_end": "1", "status": "released", "file_type": "reads", "uuid": "4665eb25-3729-446d-af3c-aab94350ed32", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122738", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122738"}]}], "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXZK3P2RC", "status": "released", "crosslinking_method": "1% Formaldehyde", "uuid": "31c56c15-8fe2-473b-a262-bf0cc6bbab24", "biosample": {"biosource_summary": "sperm", "treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBSYJKSIX6", "uuid": "eda64cd6-bf79-4083-b031-6c7b45d194a2", "biosample_type": "primary cells", "@id": "/biosamples/4DNBSYJKSIX6/", "status": "released", "display_title": "4DNBSYJKSIX6", "biosample_category": ["Primary Cells"], "biosource": [{"status": "released", "biosource_type": "primary cell", "accession": "4DNSRVGG641I", "display_title": "sperm - 4DNSRVGG641I", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRVGG641I/", "uuid": "45627f02-19f3-471a-8d69-a91893ce3997", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"@id": "/ontology-terms/CL:0000019/", "term_id": "CL:0000019", "@type": ["OntologyTerm", "Item"], "term_name": "sperm", "display_title": "sperm", "uuid": "2e3fe957-64d9-40b0-adef-4d55bf48320e", "status": "released", "synonyms": ["spermatozoon", "spermatozoid", "sperm cell"], "preferred_name": "sperm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "@type": ["OntologyTerm", "Item"], "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"display_title": "M. musculus", "name": "mouse", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_classification": "3C via Ligation", "status": "released", "display_title": "in situ Hi-C", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_subclass_short": "Hi-C", "@type": ["ExperimentType", "Item"], "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_type": "alignments", "upload_key": "92a24981-0591-4037-b98b-ed8bb779e292/4DNFI4I3FLEY.bam", "@id": "/files-processed/4DNFI4I3FLEY/", "display_title": "4DNFI4I3FLEY.bam", "md5sum": "acda9205257073c798cac321812c6732", "file_classification": "processed file", "uuid": "92a24981-0591-4037-b98b-ed8bb779e292", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/92a24981-0591-4037-b98b-ed8bb779e292/4DNFI4I3FLEY.bam", "file_format": {"display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 20056226459, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI4I3FLEY", "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFI4I3FLEY/@@download/4DNFI4I3FLEY.bam", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/2ef80453-bee2-43d5-b469-0d7b71d206d0/", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2020-01-24", "uuid": "2ef80453-bee2-43d5-b469-0d7b71d206d0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "91344505", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "14.702", "tooltip": "Percent of total reads (=13.43m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "11.87", "tooltip": "Percent of total reads (=10.84m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "35.102", "tooltip": "Percent of total reads (=32.06m)", "numberType": "percent"}, {"title": "Walks", "value": "17.085", "tooltip": "Percent of total reads (=15.61m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.081", "tooltip": "Percent of total reads (=0.07m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-02-16T13:43:24.609417+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "contact list-replicate", "upload_key": "95c7796b-cd50-4274-8e1a-0f1905a03ce1/4DNFI85GLH16.pairs.gz", "@id": "/files-processed/4DNFI85GLH16/", "display_title": "4DNFI85GLH16.pairs.gz", "md5sum": "9a9d3246acb1c4efe78120dfb1523256", "file_classification": "processed file", "uuid": "95c7796b-cd50-4274-8e1a-0f1905a03ce1", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/95c7796b-cd50-4274-8e1a-0f1905a03ce1/4DNFI85GLH16.pairs.gz", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 299037633, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI85GLH16", "file_type_detailed": "contact list-replicate (pairs)", "href": "/files-processed/4DNFI85GLH16/@@download/4DNFI85GLH16.pairs.gz", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/ed8f0702-6de4-4c77-bf95-d4a7b27d5a12/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI85GLH16/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 19402975, "display_title": "QualityMetricPairsqc from 2020-01-24", "uuid": "ed8f0702-6de4-4c77-bf95-d4a7b27d5a12", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "19402975", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "24.861", "tooltip": "Percent of filtered reads (=4.82m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "36.441", "tooltip": "Percent of filtered reads (=7.07m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "38.698", "tooltip": "Percent of filtered reads (=7.51m)", "numberType": "percent"}]}, "extra_files": [{"md5sum": "1016df2ce319f7bbfd0a01e5ac1aa593", "href": "/files-processed/4DNFI85GLH16/@@download/4DNFI85GLH16.pairs.gz.px2", "file_size": 15312679, "file_format": {"@id": "/file-formats/pairs_px2/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-04-06T20:19:10.754188+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"name": "MboI", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: MboI", "field": "Enzyme", "value": "MboI"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2020-02-07T20:07:24.420080+00:00"}, "external_references": [{"ref": "GEO:GSM2434086", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2434086"}]}, {"display_title": "in situ Hi-C on sperm with MboI - 4DNEX5M2F6X6", "@id": "/experiments-hi-c/4DNEX5M2F6X6/", "dbxrefs": ["GEO:GSM2434087"], "files": [{"file_size": 14104657869, "file_type": "reads", "uuid": "25e120ca-bcb0-41f7-99fb-96efc9bea661", "dbxrefs": ["SRA:SRR5122739"], "href": "/files-fastq/4DNFIX3VZW6N/@@download/4DNFIX3VZW6N.fastq.gz", "paired_end": "1", "accession": "4DNFIX3VZW6N", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/25e120ca-bcb0-41f7-99fb-96efc9bea661/4DNFIX3VZW6N.fastq.gz", "display_title": "4DNFIX3VZW6N.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "25e120ca-bcb0-41f7-99fb-96efc9bea661/4DNFIX3VZW6N.fastq.gz", "md5sum": "f3fd1febe879730ab1e0cc887843c7be", "@id": "/files-fastq/4DNFIX3VZW6N/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 177357363, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "06f92b3b-0df6-4144-a64b-291208c8d8ee", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/06f92b3b-0df6-4144-a64b-291208c8d8ee/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIX3VZW6N/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFI989O2PC.fastq.gz", "accession": "4DNFI989O2PC", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFI989O2PC/", "paired_end": "2", "status": "released", "file_type": "reads", "uuid": "b2a426cf-85fb-4353-b591-cd97e206524e", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122739", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122739"}]}, {"file_size": 16149192109, "file_type": "reads", "uuid": "b2a426cf-85fb-4353-b591-cd97e206524e", "dbxrefs": ["SRA:SRR5122739"], "href": "/files-fastq/4DNFI989O2PC/@@download/4DNFI989O2PC.fastq.gz", "paired_end": "2", "accession": "4DNFI989O2PC", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/b2a426cf-85fb-4353-b591-cd97e206524e/4DNFI989O2PC.fastq.gz", "display_title": "4DNFI989O2PC.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "b2a426cf-85fb-4353-b591-cd97e206524e/4DNFI989O2PC.fastq.gz", "md5sum": "03e98b61fdffab7cb43958f2359376a5", "@id": "/files-fastq/4DNFI989O2PC/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 177357363, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "7c0afa51-7009-482c-b3fd-7cee24e879c8", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/7c0afa51-7009-482c-b3fd-7cee24e879c8/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI989O2PC/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIX3VZW6N.fastq.gz", "accession": "4DNFIX3VZW6N", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIX3VZW6N/", "paired_end": "1", "status": "released", "file_type": "reads", "uuid": "25e120ca-bcb0-41f7-99fb-96efc9bea661", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122739", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122739"}]}], "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEX5M2F6X6", "status": "released", "crosslinking_method": "1% Formaldehyde", "uuid": "9e971d80-e461-4a4c-a303-7243909bcdb9", "biosample": {"biosource_summary": "sperm", "treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBS5HRO8PK", "uuid": "a84f4c81-28c6-4799-8154-71e7118ae884", "biosample_type": "primary cells", "@id": "/biosamples/4DNBS5HRO8PK/", "status": "released", "display_title": "4DNBS5HRO8PK", "biosample_category": ["Primary Cells"], "biosource": [{"status": "released", "biosource_type": "primary cell", "accession": "4DNSRVGG641I", "display_title": "sperm - 4DNSRVGG641I", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRVGG641I/", "uuid": "45627f02-19f3-471a-8d69-a91893ce3997", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"@id": "/ontology-terms/CL:0000019/", "term_id": "CL:0000019", "@type": ["OntologyTerm", "Item"], "term_name": "sperm", "display_title": "sperm", "uuid": "2e3fe957-64d9-40b0-adef-4d55bf48320e", "status": "released", "synonyms": ["spermatozoon", "spermatozoid", "sperm cell"], "preferred_name": "sperm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "@type": ["OntologyTerm", "Item"], "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"display_title": "M. musculus", "name": "mouse", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_classification": "3C via Ligation", "status": "released", "display_title": "in situ Hi-C", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_subclass_short": "Hi-C", "@type": ["ExperimentType", "Item"], "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_type": "alignments", "upload_key": "2acbd4f7-ff1c-47b1-ab92-cac00a66ef01/4DNFI4VRK3N8.bam", "@id": "/files-processed/4DNFI4VRK3N8/", "display_title": "4DNFI4VRK3N8.bam", "md5sum": "b9c94cb16332ae26d594f2e4e9963a53", "file_classification": "processed file", "uuid": "2acbd4f7-ff1c-47b1-ab92-cac00a66ef01", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/2acbd4f7-ff1c-47b1-ab92-cac00a66ef01/4DNFI4VRK3N8.bam", "file_format": {"display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 36989172426, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFI4VRK3N8", "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFI4VRK3N8/@@download/4DNFI4VRK3N8.bam", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/7f338534-95a4-40ef-83ad-e58b566e8a20/", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2020-01-24", "uuid": "7f338534-95a4-40ef-83ad-e58b566e8a20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "177357363", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "13.197", "tooltip": "Percent of total reads (=23.41m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "11.671", "tooltip": "Percent of total reads (=20.7m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "41.881", "tooltip": "Percent of total reads (=74.28m)", "numberType": "percent"}, {"title": "Walks", "value": "17.691", "tooltip": "Percent of total reads (=31.38m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.055", "tooltip": "Percent of total reads (=0.1m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-02-16T13:43:23.410724+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "contact list-replicate", "upload_key": "75185454-ef12-4c7a-8e5a-d074279ccd0a/4DNFIK41CGVD.pairs.gz", "@id": "/files-processed/4DNFIK41CGVD/", "display_title": "4DNFIK41CGVD.pairs.gz", "md5sum": "8e296dea240a9031d1ef00c4f78d3ef0", "file_classification": "processed file", "uuid": "75185454-ef12-4c7a-8e5a-d074279ccd0a", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/75185454-ef12-4c7a-8e5a-d074279ccd0a/4DNFIK41CGVD.pairs.gz", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 420970223, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIK41CGVD", "file_type_detailed": "contact list-replicate (pairs)", "href": "/files-processed/4DNFIK41CGVD/@@download/4DNFIK41CGVD.pairs.gz", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/7e738ca0-5e23-4e17-b1c7-f1c0128bc59b/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIK41CGVD/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 27596457, "display_title": "QualityMetricPairsqc from 2020-01-24", "uuid": "7e738ca0-5e23-4e17-b1c7-f1c0128bc59b", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "27596457", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "22.911", "tooltip": "Percent of filtered reads (=6.32m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "40.504", "tooltip": "Percent of filtered reads (=11.18m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "36.585", "tooltip": "Percent of filtered reads (=10.1m)", "numberType": "percent"}]}, "extra_files": [{"md5sum": "3a05faa021b00705120fcc827ff35ee7", "href": "/files-processed/4DNFIK41CGVD/@@download/4DNFIK41CGVD.pairs.gz.px2", "file_size": 16127446, "file_format": {"@id": "/file-formats/pairs_px2/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-04-06T20:19:10.139133+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"name": "MboI", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: MboI", "field": "Enzyme", "value": "MboI"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2020-02-07T20:06:41.006929+00:00"}, "external_references": [{"ref": "GEO:GSM2434087", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2434087"}]}, {"display_title": "in situ Hi-C on sperm with MboI - 4DNEXI9UU2P4", "@id": "/experiments-hi-c/4DNEXI9UU2P4/", "dbxrefs": ["GEO:GSM2434088"], "files": [{"file_size": 15322442477, "file_type": "reads", "uuid": "5bec7e21-427e-4784-a1a6-5f958d680f62", "dbxrefs": ["SRA:SRR5122740"], "href": "/files-fastq/4DNFIACVSVQZ/@@download/4DNFIACVSVQZ.fastq.gz", "paired_end": "1", "accession": "4DNFIACVSVQZ", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/5bec7e21-427e-4784-a1a6-5f958d680f62/4DNFIACVSVQZ.fastq.gz", "display_title": "4DNFIACVSVQZ.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "5bec7e21-427e-4784-a1a6-5f958d680f62/4DNFIACVSVQZ.fastq.gz", "md5sum": "d8d7d243c6179a421c03e110b20cd47f", "@id": "/files-fastq/4DNFIACVSVQZ/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 193783254, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "59f5b562-257e-411a-a9fa-372129a5b2b4", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/59f5b562-257e-411a-a9fa-372129a5b2b4/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIACVSVQZ/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIXA83BII.fastq.gz", "accession": "4DNFIXA83BII", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIXA83BII/", "paired_end": "2", "status": "released", "file_type": "reads", "uuid": "a62a7468-7650-433d-a64a-80a4e27e232d", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122740", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122740"}]}, {"file_size": 17471051319, "file_type": "reads", "uuid": "a62a7468-7650-433d-a64a-80a4e27e232d", "dbxrefs": ["SRA:SRR5122740"], "href": "/files-fastq/4DNFIXA83BII/@@download/4DNFIXA83BII.fastq.gz", "paired_end": "2", "accession": "4DNFIXA83BII", "@type": ["FileFastq", "File", "Item"], "status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/files/a62a7468-7650-433d-a64a-80a4e27e232d/4DNFIXA83BII.fastq.gz", "display_title": "4DNFIXA83BII.fastq.gz", "file_classification": "raw file", "file_type_detailed": "reads (fastq)", "upload_key": "a62a7468-7650-433d-a64a-80a4e27e232d/4DNFIXA83BII.fastq.gz", "md5sum": "44ef6cbb618c156eabdcdb07bff49351", "@id": "/files-fastq/4DNFIXA83BII/", "quality_metric": {"display_title": "QualityMetricFastqc from 2020-01-22", "Total Sequences": 193783254, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "uuid": "5c9860de-79f1-42ac-8f03-2a7a598ba793", "overall_quality_status": "PASS", "status": "released", "Sequence length": "150", "@id": "/quality-metrics-fastqc/5c9860de-79f1-42ac-8f03-2a7a598ba793/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIXA83BII/fastqc_report.html", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"display_title": "4DNFIACVSVQZ.fastq.gz", "accession": "4DNFIACVSVQZ", "file_type_detailed": "reads (fastq)", "@id": "/files-fastq/4DNFIACVSVQZ/", "paired_end": "1", "status": "released", "file_type": "reads", "uuid": "5bec7e21-427e-4784-a1a6-5f958d680f62", "@type": ["FileFastq", "File", "Item"], "file_format": {"@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "file_format": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "display_title": "fastq", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "raw file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "lab": {"display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "status": "current", "@id": "/labs/wei-xie-lab/", "name": "wei-xie-lab", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "status": "released", "file_format": "fastq", "@id": "/file-formats/fastq/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "external_references": [{"ref": "SRA:SRR5122740", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122740"}]}], "@type": ["ExperimentHiC", "Experiment", "Item"], "accession": "4DNEXI9UU2P4", "status": "released", "crosslinking_method": "1% Formaldehyde", "uuid": "50c92db2-2449-4aa4-8d93-76d9aae9b9cc", "biosample": {"biosource_summary": "sperm", "treatments_summary": "None", "modifications_summary": "None", "@type": ["Biosample", "Item"], "accession": "4DNBS4EDN9U3", "uuid": "888338a3-1560-405e-8538-43a9d4d9e126", "biosample_type": "primary cells", "@id": "/biosamples/4DNBS4EDN9U3/", "status": "released", "display_title": "4DNBS4EDN9U3", "biosample_category": ["Primary Cells"], "biosource": [{"status": "released", "biosource_type": "primary cell", "accession": "4DNSRVGG641I", "display_title": "sperm - 4DNSRVGG641I", "cell_line_tier": "Unclassified", "@type": ["Biosource", "Item"], "@id": "/biosources/4DNSRVGG641I/", "uuid": "45627f02-19f3-471a-8d69-a91893ce3997", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "cell_line": {"@id": "/ontology-terms/CL:0000019/", "term_id": "CL:0000019", "@type": ["OntologyTerm", "Item"], "term_name": "sperm", "display_title": "sperm", "uuid": "2e3fe957-64d9-40b0-adef-4d55bf48320e", "status": "released", "synonyms": ["spermatozoon", "spermatozoid", "sperm cell"], "preferred_name": "sperm", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "slim_terms": [{"status": "released", "@id": "/ontology-terms/CL:0000000/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000926/", "display_title": "mesoderm", "@type": ["OntologyTerm", "Item"], "uuid": "111120bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "released", "@id": "/ontology-terms/UBERON:0000990/", "display_title": "reproductive system", "@type": ["OntologyTerm", "Item"], "uuid": "111127bc-8535-4448-903e-854af460a233", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"status": "current", "@id": "/ontology-terms/GO:0005623/", "display_title": "cell", "@type": ["OntologyTerm", "Item"], "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}]}, "organism": {"display_title": "M. musculus", "name": "mouse", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "scientific_name": "Mus musculus", "@type": ["Organism", "Item"], "@id": "/organisms/10090/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_type": {"@id": "/experiment-types/in-situ-hi-c/", "title": "in situ Hi-C", "assay_subclassification": "DNA-DNA Pairwise Interactions", "assay_classification": "3C via Ligation", "status": "released", "display_title": "in situ Hi-C", "experiment_category": "Sequencing", "other_tags": ["DNA-DNA", "Pairwise", "3D"], "assay_subclass_short": "Hi-C", "@type": ["ExperimentType", "Item"], "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "processed_files": [{"file_type": "alignments", "upload_key": "b2111c0c-5c37-4b70-98ad-09249f94d27f/4DNFIMJ3H9EW.bam", "@id": "/files-processed/4DNFIMJ3H9EW/", "display_title": "4DNFIMJ3H9EW.bam", "md5sum": "2741b56d1c3190da40ff864a2f505ce1", "file_classification": "processed file", "uuid": "b2111c0c-5c37-4b70-98ad-09249f94d27f", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/b2111c0c-5c37-4b70-98ad-09249f94d27f/4DNFIMJ3H9EW.bam", "file_format": {"display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/bam/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 42570510395, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFIMJ3H9EW", "file_type_detailed": "alignments (bam)", "href": "/files-processed/4DNFIMJ3H9EW/@@download/4DNFIMJ3H9EW.bam", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-bamqc/d33bd53a-ef59-4c93-856e-2b7f43b17af8/", "status": "released", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "display_title": "QualityMetricBamqc from 2020-01-24", "uuid": "d33bd53a-ef59-4c93-856e-2b7f43b17af8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Total Reads", "value": "193783254", "numberType": "integer"}, {"title": "Unmapped Reads", "value": "10.762", "tooltip": "Percent of total reads (=20.86m)", "numberType": "percent"}, {"title": "Multimapped Reads", "value": "12.103", "tooltip": "Percent of total reads (=23.45m)", "numberType": "percent"}, {"title": "Duplicate Reads", "value": "37.712", "tooltip": "Percent of total reads (=73.08m)", "numberType": "percent"}, {"title": "Walks", "value": "18.828", "tooltip": "Percent of total reads (=36.48m)", "numberType": "percent"}, {"title": "Minor Contigs", "value": "0.07", "tooltip": "Percent of total reads (=0.14m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-02-16T13:43:22.261316+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type": "contact list-replicate", "upload_key": "ca5de739-01d6-41b0-87e7-5fbf38d1e4a9/4DNFII1L7W8H.pairs.gz", "@id": "/files-processed/4DNFII1L7W8H/", "display_title": "4DNFII1L7W8H.pairs.gz", "md5sum": "52a4b896a5ae54b976c1b62166b60a49", "file_classification": "processed file", "uuid": "ca5de739-01d6-41b0-87e7-5fbf38d1e4a9", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/ca5de739-01d6-41b0-87e7-5fbf38d1e4a9/4DNFII1L7W8H.pairs.gz", "file_format": {"display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@type": ["FileFormat", "Item"], "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 611532787, "genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "accession": "4DNFII1L7W8H", "file_type_detailed": "contact list-replicate (pairs)", "href": "/files-processed/4DNFII1L7W8H/@@download/4DNFII1L7W8H.pairs.gz", "status": "released", "quality_metric": {"overall_quality_status": "PASS", "@id": "/quality-metrics-pairsqc/f33bf698-3b03-4711-8f23-99aa019252b0/", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFII1L7W8H/pairsqc_report.html", "status": "released", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "Total reads": 39911445, "display_title": "QualityMetricPairsqc from 2020-01-24", "uuid": "f33bf698-3b03-4711-8f23-99aa019252b0", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "39911445", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "26.264", "tooltip": "Percent of filtered reads (=10.48m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "36.963", "tooltip": "Percent of filtered reads (=14.75m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "36.773", "tooltip": "Percent of filtered reads (=14.68m)", "numberType": "percent"}]}, "extra_files": [{"md5sum": "059f214b4f44b2ceeaab3b46ac5c9815", "href": "/files-processed/4DNFII1L7W8H/@@download/4DNFII1L7W8H.pairs.gz.px2", "file_size": 16882980, "file_format": {"@id": "/file-formats/pairs_px2/", "status": "released", "uuid": "d13d06cf-218e-4f61-aaf0-91f226348b2c", "file_format": "pairs_px2", "@type": ["FileFormat", "Item"], "display_title": "pairs_px2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "track_and_facet_info": {"experimental_lab": "Wei Xie, TSINGHUA", "experiment_type": "in situ Hi-C", "experiment_bucket": "processed file", "assay_info": "MboI", "dataset": "sisHi-C during early embryonic development", "condition": "Sperm cells", "replicate_info": "Biorep 3, Techrep 1", "biosource_name": "sperm", "lab_name": "Wei Xie, TSINGHUA"}, "external_references": [], "lab": {"status": "current", "name": "wei-xie-lab", "@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "last_modified": {"date_modified": "2021-04-06T20:19:09.290500+00:00"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "digestion_enzyme": {"name": "MboI", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "display_title": "MboI", "@type": ["Enzyme", "Item"], "status": "released", "@id": "/enzymes/MboI/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "experiment_categorizer": {"combined": "Enzyme: MboI", "field": "Enzyme", "value": "MboI"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2020-02-07T20:07:05.109900+00:00"}, "external_references": [{"ref": "GEO:GSM2434088", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2434088"}]}], "experimentset_type": "replicate", "completed_processes": ["compartments_v1.2", "HiC_Pipeline_0.2.7"], "other_processed_files": [], "@id": "/experiment-set-replicates/4DNESTRKO6LB/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "9fdfcd30-9bc0-4010-ac55-84cdd95c8b74", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "4DNESTRKO6LB", "external_references": [], "produced_in_pub": {"short_attribution": "Du Z et al. (2017)", "ID": "PMID:28703188", "status": "current", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "journal": "Nature", "date_published": "2017-07-12", "url": "https://www.ncbi.nlm.nih.gov/pubmed/28703188", "display_title": "Du Z et al. (2017) PMID:28703188", "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs) and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "@type": ["Publication", "Item"], "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "display_title": "Du Z et al. (2017) PMID:28703188", "date_published": "2017-07-12", "ID": "PMID:28703188", "authors": ["Du Z", "Zheng H", "Huang B", "Ma R", "Wu J", "Zhang X", "He J", "Xiang Y", "Wang Q", "Li Y", "Ma J", "Zhang X", "Zhang K", "Wang Y", "Zhang MQ", "Gao J", "Dixon JR", "Wang X", "Zeng J", "Xie W"], "abstract": "In mammals, chromatin organization undergoes drastic reprogramming after fertilization. However, the three-dimensional structure of chromatin and its reprogramming in preimplantation development remain poorly understood. Here, by developing a low-input Hi-C (genome-wide chromosome conformation capture) approach, we examined the reprogramming of chromatin organization during early development in mice. We found that oocytes in metaphase II show homogeneous chromatin folding that lacks detectable topologically associating domains (TADs) and chromatin compartments. Strikingly, chromatin shows greatly diminished higher-order structure after fertilization. Unexpectedly, the subsequent establishment of chromatin organization is a prolonged process that extends through preimplantation development, as characterized by slow consolidation of TADs and segregation of chromatin compartments. The two sets of parental chromosomes are spatially separated from each other and display distinct compartmentalization in zygotes. Such allele separation and allelic compartmentalization can be found as late as the 8-cell stage. Finally, we show that chromatin compaction in preimplantation embryos can partially proceed in the absence of zygotic transcription and is a multi-level hierarchical process. Taken together, our data suggest that chromatin may exist in a markedly relaxed state after fertilization, followed by progressive maturation of higher-order chromatin architecture during early development.", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "journal": "Nature", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "status": "current", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 3, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}