{"lab": {"title": "Wei Xie, TSINGHUA", "@id": "/labs/wei-xie-lab/", "display_title": "Wei Xie, TSINGHUA", "status": "current", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "award": {"uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "description": "Funding source is from outside 4DN.", "status": "current", "project": "External", "display_title": "EXTERNAL AWARD", "@id": "/awards/external-award/", "name": "external-award", "@type": ["Award", "Item"], "center": "External", "center_title": "External", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"file_type_detailed": "reads (fastq)", "file_size": 7258409644, "accession": "4DNFIJSJTQWR", "display_title": "4DNFIJSJTQWR.fastq.gz", "href": "/files-fastq/4DNFIJSJTQWR/@@download/4DNFIJSJTQWR.fastq.gz", "uuid": "4665eb25-3729-446d-af3c-aab94350ed32", "status": "released", "dbxrefs": ["SRA:SRR5122738"], "file_type": "reads", "@id": "/files-fastq/4DNFIJSJTQWR/", "upload_key": "4665eb25-3729-446d-af3c-aab94350ed32/4DNFIJSJTQWR.fastq.gz", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "paired_end": "1", "quality_metric": {"Sequence length": "150", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2020-01-22", "@id": "/quality-metrics-fastqc/896bb40f-6b37-4f0c-a6fb-6d9d02811492/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJSJTQWR/fastqc_report.html", "uuid": "896bb40f-6b37-4f0c-a6fb-6d9d02811492", "Total Sequences": 91344505, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "paired_end": "2", "file_type_detailed": "reads (fastq)", "accession": "4DNFIMG5GS2I", "status": "released", "@id": "/files-fastq/4DNFIMG5GS2I/", "file_type": "reads", "uuid": "de34add4-672f-4f2b-b772-1fd0989f5303", "display_title": "4DNFIMG5GS2I.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR5122738", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122738"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "reads (fastq)", "file_size": 8315208607, "accession": "4DNFIMG5GS2I", "display_title": "4DNFIMG5GS2I.fastq.gz", "href": "/files-fastq/4DNFIMG5GS2I/@@download/4DNFIMG5GS2I.fastq.gz", "uuid": "de34add4-672f-4f2b-b772-1fd0989f5303", "status": "released", "dbxrefs": ["SRA:SRR5122738"], "file_type": "reads", "@id": "/files-fastq/4DNFIMG5GS2I/", "upload_key": "de34add4-672f-4f2b-b772-1fd0989f5303/4DNFIMG5GS2I.fastq.gz", "file_classification": "raw file", "@type": ["FileFastq", "File", "Item"], "paired_end": "2", "quality_metric": {"Sequence length": "150", "status": "released", "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2020-01-22", "@id": "/quality-metrics-fastqc/0f5e068a-44a1-4cba-a843-10f8e6ec629e/", "overall_quality_status": "PASS", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIMG5GS2I/fastqc_report.html", "uuid": "0f5e068a-44a1-4cba-a843-10f8e6ec629e", "Total Sequences": 91344505, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_format": {"@type": ["FileFormat", "Item"], "file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "display_title": "fastq", "uuid": "c13d06cf-218e-4f61-aaf0-91f226248b2c", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "related_files": [{"relationship_type": "paired with", "file": {"@type": ["FileFastq", "File", "Item"], "paired_end": "1", "file_type_detailed": "reads (fastq)", "accession": "4DNFIJSJTQWR", "status": "released", "@id": "/files-fastq/4DNFIJSJTQWR/", "file_type": "reads", "uuid": "4665eb25-3729-446d-af3c-aab94350ed32", "display_title": "4DNFIJSJTQWR.fastq.gz", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "external_references": [{"ref": "SRA:SRR5122738", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRR5122738"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "status": "released", "aliases": ["4dn-dcic-lab:GSM2434086"], "dbxrefs": ["GEO:GSM2434086"], "protocol": {"display_title": "Small-scale in situ Hi-C", "@type": ["Protocol", "Item"], "status": "released", "uuid": "250cabce-798c-4375-a58b-47bd4617e009", "@id": "/protocols/250cabce-798c-4375-a58b-47bd4617e009/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEXZK3P2RC", "biosample": {"status": "released", "uuid": "eda64cd6-bf79-4083-b031-6c7b45d194a2", "biosource_summary": "sperm", "biosample_type": "primary cells", "display_title": "4DNBSYJKSIX6", "@type": ["Biosample", "Item"], "accession": "4DNBSYJKSIX6", "modifications_summary": "None", "@id": "/biosamples/4DNBSYJKSIX6/", "treatments_summary": "None", "biosource": [{"lab": {"@id": "/labs/wei-xie-lab/", "@type": ["Lab", "Item"], "display_title": "Wei Xie, TSINGHUA", "status": "current", "uuid": "8c95312f-afa0-49ee-9d3c-e30849c74e50", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "submits_for.8c95312f-afa0-49ee-9d3c-e30849c74e50"]}}, "award": {"display_title": "EXTERNAL AWARD", "@type": ["Award", "Item"], "uuid": "12a92962-8265-4fc0-b2f8-cf14f05db58b", "@id": "/awards/external-award/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "aliases": ["4dn-dcic-lab:sperm-PWK-PhJ"], "accession": "4DNSRVGG641I", "cell_line": {"status": "released", "@type": ["OntologyTerm", "Item"], "display_title": "sperm", "preferred_name": "sperm", "synonyms": ["spermatozoon", "spermatozoid", "sperm cell"], "@id": "/ontology-terms/CL:0000019/", "term_name": "sperm", "uuid": "2e3fe957-64d9-40b0-adef-4d55bf48320e", "term_id": "CL:0000019", "slim_terms": [{"@id": "/ontology-terms/CL:0000000/", "uuid": "45d2b02e-130b-40db-8bf2-2288c6c57dcf", "display_title": "cell", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000926/", "uuid": "111120bc-8535-4448-903e-854af460a233", "display_title": "mesoderm", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000990/", "uuid": "111127bc-8535-4448-903e-854af460a233", "display_title": "reproductive system", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/GO:0005623/", "uuid": "72e16a19-eef3-46ca-a1b8-20e646e69675", "display_title": "cell", "status": "released", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "individual": {"status": "released", "@type": ["IndividualMouse", "Individual", "Item"], "@id": "/individuals-mouse/4DNINW9A7AGM/", "display_title": "4DNINW9A7AGM", "uuid": "889d33e2-4935-4f10-b33d-13c316cbff88", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Mature mouse sperm cells from 8-week old wild-type males of PWK/PhJ background", "date_created": "2020-01-10T15:41:26.997830+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-02-07T20:14:41.466186+00:00"}, "biosource_type": "primary cell", "cell_line_tier": "Unclassified", "public_release": "2020-02-07", "schema_version": "2", "project_release": "2020-02-07", "@id": "/biosources/4DNSRVGG641I/", "@type": ["Biosource", "Item"], "uuid": "45627f02-19f3-471a-8d69-a91893ce3997", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "sperm - 4DNSRVGG641I", "external_references": [], "biosource_name": "sperm", "biosource_category": ["Primary Cells"], "organism": {"@type": ["Organism", "Item"], "name": "mouse", "@id": "/organisms/10090/", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "display_title": "M. musculus", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 15, "description": "sisHi-C of mouse sperm cells, replicate 1", "sop_mapping": {"has_sop": "No"}, "date_created": "2020-01-10T15:43:10.980546+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2020-02-07T20:07:24.420080+00:00"}, "ligation_time": 360.0, "digestion_time": 960.0, "public_release": "2020-02-07", "schema_version": "2", "tagging_method": "biotin-14-dCTP", "experiment_type": {"experiment_category": "Sequencing", "status": "released", "title": "in situ Hi-C", "uuid": "a2920a38-cdba-4ff0-b4f0-c6bb53257747", "assay_subclass_short": "Hi-C", "display_title": "in situ Hi-C", "@id": "/experiment-types/in-situ-hi-c/", "@type": ["ExperimentType", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "ligation_volume": 0.12, "processed_files": [{"status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/92a24981-0591-4037-b98b-ed8bb779e292/4DNFI4I3FLEY.bam", "upload_key": "92a24981-0591-4037-b98b-ed8bb779e292/4DNFI4I3FLEY.bam", "display_title": "4DNFI4I3FLEY.bam", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "bam", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "@id": "/file-formats/bam/", "file_format": "bam", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 20056226459, "file_type": "alignments", "@id": "/files-processed/4DNFI4I3FLEY/", "@type": ["FileProcessed", "File", "Item"], "uuid": "92a24981-0591-4037-b98b-ed8bb779e292", "file_classification": "processed file", "href": "/files-processed/4DNFI4I3FLEY/@@download/4DNFI4I3FLEY.bam", "accession": "4DNFI4I3FLEY", "file_type_detailed": "alignments (bam)", "quality_metric": {"status": "released", "@id": "/quality-metrics-bamqc/2ef80453-bee2-43d5-b469-0d7b71d206d0/", "display_title": "QualityMetricBamqc from 2020-01-24", "@type": ["QualityMetricBamqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "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"}]}, "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": []}, {"status": "released", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/95c7796b-cd50-4274-8e1a-0f1905a03ce1/4DNFI85GLH16.pairs.gz", "upload_key": "95c7796b-cd50-4274-8e1a-0f1905a03ce1/4DNFI85GLH16.pairs.gz", "display_title": "4DNFI85GLH16.pairs.gz", "file_format": {"@type": ["FileFormat", "Item"], "status": "released", "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "@id": "/file-formats/pairs/", "file_format": "pairs", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "file_size": 299037633, "file_type": "contact list-replicate", "@id": "/files-processed/4DNFI85GLH16/", "@type": ["FileProcessed", "File", "Item"], "uuid": "95c7796b-cd50-4274-8e1a-0f1905a03ce1", "file_classification": "processed file", "href": "/files-processed/4DNFI85GLH16/@@download/4DNFI85GLH16.pairs.gz", "accession": "4DNFI85GLH16", "file_type_detailed": "contact list-replicate (pairs)", "quality_metric": {"status": "released", "@id": "/quality-metrics-pairsqc/ed8f0702-6de4-4c77-bf95-d4a7b27d5a12/", "display_title": "QualityMetricPairsqc from 2020-01-24", "@type": ["QualityMetricPairsqc", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "ed8f0702-6de4-4c77-bf95-d4a7b27d5a12", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI85GLH16/pairsqc_report.html", "Total reads": 19402975, "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"}]}, "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": []}], "project_release": "2020-02-07", "digestion_enzyme": {"@type": ["Enzyme", "Item"], "name": "MboI", "@id": "/enzymes/MboI/", "uuid": "d8da42d0-bc20-40e5-bacf-c263b8603e03", "status": "released", "display_title": "MboI", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "crosslinking_time": 10.0, "crosslinking_method": "1% Formaldehyde", "fragment_size_range": "200-1000", "fragmentation_method": "shearing", "ligation_temperature": 25.0, "digestion_temperature": 37.0, "crosslinking_temperature": 25.0, "@id": "/experiments-hi-c/4DNEXZK3P2RC/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "31c56c15-8fe2-473b-a262-bf0cc6bbab24", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on sperm with MboI - 4DNEXZK3P2RC", "external_references": [{"ref": "GEO:GSM2434086", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2434086"}], "experiment_sets": [{"display_title": "4DNESTRKO6LB", "status": "released", "@id": "/experiment-set-replicates/4DNESTRKO6LB/", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "uuid": "9fdfcd30-9bc0-4010-ac55-84cdd95c8b74", "accession": "4DNESTRKO6LB", "experimentset_type": "replicate", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"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.", "display_title": "Du Z et al. (2017) PMID:28703188", "@type": ["Publication", "Item"], "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "journal": "Nature", "date_published": "2017-07-12", "short_attribution": "Du Z et al. (2017)", "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"], "status": "current", "ID": "PMID:28703188", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"journal": "Nature", "@type": ["Publication", "Item"], "display_title": "Du Z et al. (2017) PMID:28703188", "status": "current", "title": "Allelic reprogramming of 3D chromatin architecture during early mammalian development.", "uuid": "7b570ea3-1ca6-4076-83a3-666d35819cf1", "short_attribution": "Du Z et al. (2017)", "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.", "date_published": "2017-07-12", "@id": "/publications/7b570ea3-1ca6-4076-83a3-666d35819cf1/", "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"], "ID": "PMID:28703188", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "MboI", "combined": "Enzyme: MboI"}, "experiment_summary": "in situ Hi-C on sperm with MboI", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}