{"lab": {"@type": ["Lab", "Item"], "status": "current", "title": "Tomoko Yamada, NW", "correspondence": [{"contact_email": "dG9tb2tvLnlhbWFkYUBub3J0aHdlc3Rlcm4uZWR1", "@id": "/users/3b5a8696-b152-4a12-bcf1-69186d6bb510/", "display_title": "Tomoko Yamada"}], "uuid": "4e87e04c-6a49-4a71-8240-5fdae2f04b24", "display_title": "Tomoko Yamada, NW", "@id": "/labs/tomoko-yamada-lab/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4e87e04c-6a49-4a71-8240-5fdae2f04b24"]}}, "award": {"description": "NI-OFHHD: The long-term goals of the proposed research are to elucidate mechanisms of three-dimensional genome architecture in the control of neuronal connectivity in the brain. It has recently been found that physiological stimuli including sensory experience or developmental signals remodel neuronal genome architecture in vivo. Strikingly, it's found that long-distance genome interactions massively increase in the developing cerebellum in mice. The discovery of these long-distance interactions formed between genes critical for neuronal differentiation unveils novel nuclear mechanisms by which genome architecture may play a role in the wiring of the brain. These findings raise fundamental questions on the mechanisms and biological functions of these interactions in the brain, which will be addressed in this grant. First, the organizing principles of long-distance genome interactions in the brain will be elucidated. Based on the in vivo findings, the hypothesis that long-distance genomic interactions are organized by specific epigenetic and transcriptional features will be tested. In addition, the study will also test the hypothesis that anchors of long-distance interactions assemble into higher-ordered subnuclear structures including nuclear speckles or Mediator condensates, which function as transcriptionally active hubs. Second, the projcet will define mechanisms by which long-distance interactions are formed in development. The BAF chromatin remodeling complex alters the genome environment to activate or repress transcription and is required for brain development in mice and humans, and its dysregulation results in human neurodevelopmental disorders, including Coffin\u2013Siris syndrome and autism. Based on our preliminary findings, the hypothesis that the BAF complex transiently inhibits formation of long-distance genome interactions in immature neurons of the developing brain will be tested. Following early development, the inhibition of the long-distance interactions might be relieved by the recruitment of specific sets of transcription factors that drive terminal neuron differentiation. This project will test the hypothesis that these transcription regulators, identified using DNA motif analyses, promote the formation of the long-distance genome interactions. Finally, this study will also test the hypothesis that the formation of long-distance genome interactions is necessary for the maturation of neurons in vivo, including making proper connections with their pre- and post-synaptic partners. The proposed research is significant as it will advance our understanding of the mechanisms regulating genome architecture to control neuronal differentiation in mammalian brain. Furthermore, these studies will provide an integrated view on how genome folding in the nucleus orchestrates the assembly of neural circuits underlying behavior.", "project": "4DN", "status": "current", "@type": ["Award", "Item"], "name": "1U01DA053691-01", "center_title": "Yamada", "display_title": "MECHANISMS OF GENOME ORGANIZATION IN BRAIN DEVELOPMENT AND BEHAVIOR", "uuid": "cf1cc388-e816-4061-b354-61bc4f8a23f8", "@id": "/awards/1U01DA053691-01/", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "files": [{"paired_end": "1", "uuid": "801a3676-d2aa-450a-8562-5639b4fced40", "@id": "/files-fastq/4DNFITWSFEQ8/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFITWSFEQ8", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 36257475430, "display_title": "4DNFITWSFEQ8.fastq.gz", "href": "/files-fastq/4DNFITWSFEQ8/@@download/4DNFITWSFEQ8.fastq.gz", "upload_key": "801a3676-d2aa-450a-8562-5639b4fced40/4DNFITWSFEQ8.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "4ac3ba82-4079-4f1e-ba60-e606c124951b", "status": "released", "@id": "/files-fastq/4DNFI3GIT5I4/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI3GIT5I4.fastq.gz", "file_type": "reads", "accession": "4DNFI3GIT5I4", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "0312c77e-9c68-4b7a-8e62-731c88eee91c", "Sequence length": "151", "Total Sequences": 456620940, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFITWSFEQ8/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/0312c77e-9c68-4b7a-8e62-731c88eee91c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "4ac3ba82-4079-4f1e-ba60-e606c124951b", "@id": "/files-fastq/4DNFI3GIT5I4/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFI3GIT5I4", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 36729503431, "display_title": "4DNFI3GIT5I4.fastq.gz", "href": "/files-fastq/4DNFI3GIT5I4/@@download/4DNFI3GIT5I4.fastq.gz", "upload_key": "4ac3ba82-4079-4f1e-ba60-e606c124951b/4DNFI3GIT5I4.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "801a3676-d2aa-450a-8562-5639b4fced40", "status": "released", "@id": "/files-fastq/4DNFITWSFEQ8/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFITWSFEQ8.fastq.gz", "file_type": "reads", "accession": "4DNFITWSFEQ8", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "60bfea7b-1453-4e1c-826d-8febadc8dbdf", "Sequence length": "151", "Total Sequences": 456620940, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI3GIT5I4/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/60bfea7b-1453-4e1c-826d-8febadc8dbdf/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "1", "uuid": "a9b551a9-efda-4e2d-bf3c-ce57174692fb", "@id": "/files-fastq/4DNFIT91T3TK/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIT91T3TK", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 37919666569, "display_title": "4DNFIT91T3TK.fastq.gz", "href": "/files-fastq/4DNFIT91T3TK/@@download/4DNFIT91T3TK.fastq.gz", "upload_key": "a9b551a9-efda-4e2d-bf3c-ce57174692fb/4DNFIT91T3TK.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "ec8a9977-9569-4110-a17e-325be905e99c", "status": "released", "@id": "/files-fastq/4DNFIBWEEBYW/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIBWEEBYW.fastq.gz", "file_type": "reads", "accession": "4DNFIBWEEBYW", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "f99fe393-973a-4802-aa47-9624d1483c59", "Sequence length": "151", "Total Sequences": 443119592, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIT91T3TK/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/f99fe393-973a-4802-aa47-9624d1483c59/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "ec8a9977-9569-4110-a17e-325be905e99c", "@id": "/files-fastq/4DNFIBWEEBYW/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIBWEEBYW", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 35910559145, "display_title": "4DNFIBWEEBYW.fastq.gz", "href": "/files-fastq/4DNFIBWEEBYW/@@download/4DNFIBWEEBYW.fastq.gz", "upload_key": "ec8a9977-9569-4110-a17e-325be905e99c/4DNFIBWEEBYW.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "a9b551a9-efda-4e2d-bf3c-ce57174692fb", "status": "released", "@id": "/files-fastq/4DNFIT91T3TK/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIT91T3TK.fastq.gz", "file_type": "reads", "accession": "4DNFIT91T3TK", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "662d4ba3-0e09-400c-b82e-d9283b42a866", "Sequence length": "151", "Total Sequences": 443119592, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIBWEEBYW/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/662d4ba3-0e09-400c-b82e-d9283b42a866/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "1", "uuid": "9c40de1e-a9ce-4ba9-a749-cf0cdc76e11b", "@id": "/files-fastq/4DNFINTF8OVU/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFINTF8OVU", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 40028872010, "display_title": "4DNFINTF8OVU.fastq.gz", "href": "/files-fastq/4DNFINTF8OVU/@@download/4DNFINTF8OVU.fastq.gz", "upload_key": "9c40de1e-a9ce-4ba9-a749-cf0cdc76e11b/4DNFINTF8OVU.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "7701f91f-9a12-4e26-90ae-75932902253d", "status": "released", "@id": "/files-fastq/4DNFIGJHU58S/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIGJHU58S.fastq.gz", "file_type": "reads", "accession": "4DNFIGJHU58S", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "19feacc4-9024-4f7f-97b6-ff7d7b64c6c6", "Sequence length": "151", "Total Sequences": 484151717, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFINTF8OVU/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/19feacc4-9024-4f7f-97b6-ff7d7b64c6c6/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "7701f91f-9a12-4e26-90ae-75932902253d", "@id": "/files-fastq/4DNFIGJHU58S/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIGJHU58S", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 40223469809, "display_title": "4DNFIGJHU58S.fastq.gz", "href": "/files-fastq/4DNFIGJHU58S/@@download/4DNFIGJHU58S.fastq.gz", "upload_key": "7701f91f-9a12-4e26-90ae-75932902253d/4DNFIGJHU58S.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "9c40de1e-a9ce-4ba9-a749-cf0cdc76e11b", "status": "released", "@id": "/files-fastq/4DNFINTF8OVU/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFINTF8OVU.fastq.gz", "file_type": "reads", "accession": "4DNFINTF8OVU", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "ad2b9f46-c34f-4bd9-a3c2-cdf1384ff38f", "Sequence length": "151", "Total Sequences": 484151717, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIGJHU58S/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/ad2b9f46-c34f-4bd9-a3c2-cdf1384ff38f/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "1", "uuid": "51c278f5-66ad-4c5d-bc36-84d284d61106", "@id": "/files-fastq/4DNFIETN73WX/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIETN73WX", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 36604160324, "display_title": "4DNFIETN73WX.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads"], "href": "/files-fastq/4DNFIETN73WX/@@download/4DNFIETN73WX.fastq.gz", "upload_key": "51c278f5-66ad-4c5d-bc36-84d284d61106/4DNFIETN73WX.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "36d815bb-42f8-41bf-8928-033c17ef46cd", "status": "released", "@id": "/files-fastq/4DNFIO6GLED2/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIO6GLED2.fastq.gz", "file_type": "reads", "accession": "4DNFIO6GLED2", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "f2ff10db-6aab-4455-8a0f-de37a8857e3c", "Sequence length": "151", "Total Sequences": 433424390, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIETN73WX/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/f2ff10db-6aab-4455-8a0f-de37a8857e3c/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "36d815bb-42f8-41bf-8928-033c17ef46cd", "@id": "/files-fastq/4DNFIO6GLED2/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIO6GLED2", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 35561622842, "display_title": "4DNFIO6GLED2.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads"], "href": "/files-fastq/4DNFIO6GLED2/@@download/4DNFIO6GLED2.fastq.gz", "upload_key": "36d815bb-42f8-41bf-8928-033c17ef46cd/4DNFIO6GLED2.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "51c278f5-66ad-4c5d-bc36-84d284d61106", "status": "released", "@id": "/files-fastq/4DNFIETN73WX/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIETN73WX.fastq.gz", "file_type": "reads", "accession": "4DNFIETN73WX", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "eed9b9f8-52e2-4fe3-aea4-853c46de78f2", "Sequence length": "151", "Total Sequences": 433424390, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIO6GLED2/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/eed9b9f8-52e2-4fe3-aea4-853c46de78f2/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "1", "uuid": "8a37e78d-864c-4b68-8d47-ce1f334e0720", "@id": "/files-fastq/4DNFIQTFV581/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIQTFV581", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 35219183808, "display_title": "4DNFIQTFV581.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads"], "href": "/files-fastq/4DNFIQTFV581/@@download/4DNFIQTFV581.fastq.gz", "upload_key": "8a37e78d-864c-4b68-8d47-ce1f334e0720/4DNFIQTFV581.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "496e2019-e6b5-4b79-8838-7f83a4e40210", "status": "released", "@id": "/files-fastq/4DNFI6DUFV1O/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFI6DUFV1O.fastq.gz", "file_type": "reads", "accession": "4DNFI6DUFV1O", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "41e5e54a-acc7-4151-b899-b6f636254767", "Sequence length": "151", "Total Sequences": 414412809, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIQTFV581/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/41e5e54a-acc7-4151-b899-b6f636254767/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "496e2019-e6b5-4b79-8838-7f83a4e40210", "@id": "/files-fastq/4DNFI6DUFV1O/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFI6DUFV1O", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 34058235513, "display_title": "4DNFI6DUFV1O.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads"], "href": "/files-fastq/4DNFI6DUFV1O/@@download/4DNFI6DUFV1O.fastq.gz", "upload_key": "496e2019-e6b5-4b79-8838-7f83a4e40210/4DNFI6DUFV1O.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "8a37e78d-864c-4b68-8d47-ce1f334e0720", "status": "released", "@id": "/files-fastq/4DNFIQTFV581/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIQTFV581.fastq.gz", "file_type": "reads", "accession": "4DNFIQTFV581", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "9908e871-a93a-458b-a513-49c151ea4830", "Sequence length": "151", "Total Sequences": 414412809, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-25", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFI6DUFV1O/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/9908e871-a93a-458b-a513-49c151ea4830/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "1", "uuid": "907d33f7-6e6e-4ed8-a781-73c3dcc1217f", "@id": "/files-fastq/4DNFIC7SBR51/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIC7SBR51", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 196968667385, "display_title": "4DNFIC7SBR51.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads"], "href": "/files-fastq/4DNFIC7SBR51/@@download/4DNFIC7SBR51.fastq.gz", "upload_key": "907d33f7-6e6e-4ed8-a781-73c3dcc1217f/4DNFIC7SBR51.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "2", "uuid": "135a8f28-105c-400c-9767-5932afdec2f8", "status": "released", "@id": "/files-fastq/4DNFIW7H63J9/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIW7H63J9.fastq.gz", "file_type": "reads", "accession": "4DNFIW7H63J9", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "b82ba2a4-886c-4321-91be-2dfee20a28da", "Sequence length": "151", "Total Sequences": 2497407691, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-05-24", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIC7SBR51/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/b82ba2a4-886c-4321-91be-2dfee20a28da/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}, {"paired_end": "2", "uuid": "135a8f28-105c-400c-9767-5932afdec2f8", "@id": "/files-fastq/4DNFIW7H63J9/", "file_type_detailed": "reads (fastq)", "file_classification": "raw file", "accession": "4DNFIW7H63J9", "@type": ["FileFastq", "File", "Item"], "status": "released", "file_size": 186158182331, "display_title": "4DNFIW7H63J9.fastq.gz", "notes_to_tsv": ["This file contains reads from multiple biological replicates - barcode information must be used to obtain replicate-specific reads."], "href": "/files-fastq/4DNFIW7H63J9/@@download/4DNFIW7H63J9.fastq.gz", "upload_key": "135a8f28-105c-400c-9767-5932afdec2f8/4DNFIW7H63J9.fastq.gz", "file_type": "reads", "related_files": [{"relationship_type": "paired with", "file": {"paired_end": "1", "uuid": "907d33f7-6e6e-4ed8-a781-73c3dcc1217f", "status": "released", "@id": "/files-fastq/4DNFIC7SBR51/", "file_type_detailed": "reads (fastq)", "@type": ["FileFastq", "File", "Item"], "display_title": "4DNFIC7SBR51.fastq.gz", "file_type": "reads", "accession": "4DNFIC7SBR51", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "file_format": {"file_format": "fastq", "@id": "/file-formats/fastq/", "status": "released", "@type": ["FileFormat", "Item"], "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"]}, "external_references": [], "quality_metric": {"overall_quality_status": "PASS", "uuid": "518c7063-1a01-4e15-901f-b1d79ef62863", "Sequence length": "151", "Total Sequences": 2497407691, "@type": ["QualityMetricFastqc", "QualityMetric", "Item"], "display_title": "QualityMetricFastqc from 2022-04-26", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIW7H63J9/fastqc_report.html", "status": "released", "@id": "/quality-metrics-fastqc/518c7063-1a01-4e15-901f-b1d79ef62863/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "status": "released", "aliases": ["yamada-lab:experiment_sprite-mouse-cerebellum-pnd22_B1_T1"], "protocol": {"status": "released", "uuid": "4759d660-3279-49ad-8004-477bf0c4e20d", "display_title": "SPRITE_Protocol_DNA_August_2018.pdf", "@type": ["Protocol", "Item"], "@id": "/protocols/4759d660-3279-49ad-8004-477bf0c4e20d/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "accession": "4DNEX2BYUC69", "biosample": {"display_title": "4DNBSIYCHYPA", "status": "released", "biosample_type": "tissue", "@id": "/biosamples/4DNBSIYCHYPA/", "@type": ["Biosample", "Item"], "uuid": "da81f814-9d26-480e-ba40-b43af10e2e04", "modifications_summary": "None", "accession": "4DNBSIYCHYPA", "biosource_summary": "cerebellum - PND 22", "treatments_summary": "None", "biosource": [{"lab": {"display_title": "Tomoko Yamada, NW", "uuid": "4e87e04c-6a49-4a71-8240-5fdae2f04b24", "@id": "/labs/tomoko-yamada-lab/", "status": "current", "@type": ["Lab", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4e87e04c-6a49-4a71-8240-5fdae2f04b24"]}}, "award": {"uuid": "cf1cc388-e816-4061-b354-61bc4f8a23f8", "@id": "/awards/1U01DA053691-01/", "display_title": "MECHANISMS OF GENOME ORGANIZATION IN BRAIN DEVELOPMENT AND BEHAVIOR", "@type": ["Award", "Item"], "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "status": "released", "tissue": {"@id": "/ontology-terms/UBERON:0002037/", "preferred_name": "cerebellum", "status": "released", "uuid": "16b8a20c-0abf-4d6a-afc3-f5522c15c77e", "term_name": "cerebellum", "synonyms": ["epencephalon-1"], "@type": ["OntologyTerm", "Item"], "display_title": "cerebellum", "slim_terms": [{"@id": "/ontology-terms/UBERON:0000924/", "uuid": "111119bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "ectoderm", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0001017/", "uuid": "111136bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "central nervous system", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@id": "/ontology-terms/UBERON:0000955/", "uuid": "111170bc-8535-4448-903e-854af460a233", "status": "released", "display_title": "brain", "@type": ["OntologyTerm", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "term_id": "UBERON:0002037", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "aliases": ["yamada-lab:c57bl6_pnd22_cerebellum"], "accession": "4DNSRKEGZR3R", "individual": {"status": "released", "@id": "/individuals-mouse/4DNINNLYL3U2/", "uuid": "ca7bc788-be17-4020-ad9e-745fedbd2eac", "display_title": "4DNINNLYL3U2", "@type": ["IndividualMouse", "Individual", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "description": "Cerebellum from post natal day 22 C57Bl/6 mice", "date_created": "2022-03-03T14:59:30.195587+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-07T21:59:41.755027+00:00"}, "biosource_type": "tissue", "cell_line_tier": "Unclassified", "public_release": "2024-03-07", "schema_version": "2", "project_release": "2022-04-06", "override_biosource_name": "cerebellum - PND 22", "@id": "/biosources/4DNSRKEGZR3R/", "@type": ["Biosource", "Item"], "uuid": "cc1fedaa-50ae-4c47-9d6a-b2b75e67ebb7", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "cerebellum - PND 22 - 4DNSRKEGZR3R", "external_references": [], "biosource_name": "cerebellum - PND 22", "biosource_category": ["Multicellular Tissue"], "organism": {"@type": ["Organism", "Item"], "name": "mouse", "@id": "/organisms/10090/", "display_title": "M. musculus", "status": "released", "uuid": "3413218c-3d86-498b-a0a2-9a406638e786", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pcr_cycles": 11, "sop_mapping": {"has_sop": "No"}, "date_created": "2022-04-25T17:01:53.271477+00:00", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-03-07T21:57:55.219890+00:00"}, "public_release": "2024-03-07", "schema_version": "5", "tagging_rounds": 5, "experiment_type": {"title": "DNA SPRITE", "@type": ["ExperimentType", "Item"], "display_title": "DNA SPRITE", "uuid": "4004ae76-2f5c-42b6-9f72-488f60963f04", "status": "released", "experiment_category": "Sequencing", "assay_subclass_short": "Ligation-free 3C", "@id": "/experiment-types/dna-sprite/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "project_release": "2022-06-10", "reference_files": [{"file_type_detailed": "barcodes (txt)", "accession": "4DNFIMTHO6KQ", "status": "released", "file_size": 15782, "display_title": "4DNFIMTHO6KQ.txt", "file_type": "barcodes", "notes_to_tsv": ["The information in this file can be used in conjunction with that of the accompany sequencing barcode file to de-multiplex the reads in the fastq files associated with this dataset. \u00a0The same files can be used in SPRITE cluster analysis to identify and aggregate reads that belong to the same clusters. \u00a0Information about the replicate experiment and file should be used for both operations as there are barcoded reads that are included that are derived from different conditions used for the final replicates in this dataset so should not be used in final analyses. \u00a0This is in addition to some of the fastq files - as noted - that include reads from both bio replicate experiments - necessitating de-multiplexing to resolve replicate specific reads. \u00a0Please contact the Yamada lab with questions."], "uuid": "db314ebb-a011-48f1-820f-d2b125725e2d", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "@id": "/files-reference/4DNFIMTHO6KQ/", "file_format": {"@id": "/file-formats/txt/", "status": "released", "file_format": "txt", "display_title": "txt", "@type": ["FileFormat", "Item"], "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"file_type_detailed": "barcodes (txt)", "accession": "4DNFIY3DAMZF", "status": "released", "file_size": 5029, "display_title": "4DNFIY3DAMZF.txt", "file_type": "barcodes", "notes_to_tsv": ["The information in this file can be used in conjunction with that of the accompany DPM barcode file to de-multiplex the reads in the fastq files associated with this dataset. \u00a0The same files can be used in SPRITE cluster analysis to identify and aggregate reads that belong to the same clusters. \u00a0Information about the replicate experiment and file should be used for both operations as there are barcoded reads that are included that are derived from different conditions used for the final replicates in this dataset so should not be used in final analyses. \u00a0This is in addition to some of the fastq files - as noted - that include reads from both bio replicate experiments - necessitating de-multiplexing to resolve replicate specific reads. \u00a0Please contact the Yamada lab with questions."], "uuid": "777168a9-334d-4e69-87ec-63c9caacef47", "@type": ["FileReference", "File", "Item"], "file_classification": "ancillary file", "@id": "/files-reference/4DNFIY3DAMZF/", "file_format": {"@id": "/file-formats/txt/", "status": "released", "file_format": "txt", "display_title": "txt", "@type": ["FileFormat", "Item"], "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "protocol_variation": [{"@id": "/protocols/fdcbb457-38ea-42cb-a9e9-6f54ef074294/", "display_title": "Yamada lab supplemental SPRITE protocol info", "@type": ["Protocol", "Item"], "status": "released", "uuid": "fdcbb457-38ea-42cb-a9e9-6f54ef074294", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "fragment_size_range": "100-300", "fragmentation_method": "see protocol document", "average_fragment_size": 200, "other_processed_files": [{"type": "supplementary", "files": [{"genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIKU1JTFL.mcool", "higlass_uid": "649f56cb-8897-442e-a71f-339d8a0263db", "accession": "4DNFIKU1JTFL", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a5efb123-95ee-43c6-86a8-eb9cf1e0a6cb/4DNFIKU1JTFL.mcool", "uuid": "a5efb123-95ee-43c6-86a8-eb9cf1e0a6cb", "@id": "/files-processed/4DNFIKU1JTFL/", "status": "released", "file_size": 10829812577, "notes_to_tsv": ["This mcool matrix file was generated from the file 4DNFIZERUF7M containing clusters of sizes from 2-1000 generated by the Yamada lab by the 4DN-DCIC using cooler version 0.8.11 scripts based on this gist: https://gist.github.com/nvictus/aacf3530b95251e1a0945a7e36fa28ac and the zoomify function", "This file contains processed results performed outside of the 4DN-DCIC standardized pipelines. The file and the information about its provenance, i.e. which files were used as input to generate this output was provided by or done in collaboration with the lab that did the experiments to generate the raw data. For more information about the specific analysis performed, please contact the submitting lab or refer to the relevant publication if available.", "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."], "href": "/files-processed/4DNFIKU1JTFL/@@download/4DNFIKU1JTFL.mcool", "file_type_detailed": "contact matrix (mcool)", "file_type": "contact matrix", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "d13d06cf-218e-4f61-ccf0-91f226248b2c", "file_format": "mcool", "@id": "/file-formats/mcool/", "display_title": "mcool", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "quality_metric": {"status": "released", "display_title": "QualityMetricMcool from 2022-06-01", "@type": ["QualityMetricMcool", "QualityMetric", "Item"], "overall_quality_status": "PASS", "uuid": "4c8d813a-120b-4486-a8b0-cdf31c6ee625", "@id": "/quality-metrics-mcool/4c8d813a-120b-4486-a8b0-cdf31c6ee625/", "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": [{"location": "tab:higlass", "description": "auto_generated_higlass_view_config", "content": {"status": "released", "display_title": "4DNFIKU1JTFL - contact matrix for cerebellum - PND 22 DNA SPRITE", "uuid": "1dab52a0-cead-4a12-87ed-bed28338db23", "@type": ["HiglassViewConfig", "UserContent", "Item"], "@id": "/higlass-view-configs/1dab52a0-cead-4a12-87ed-bed28338db23/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.7677f8a8-79d2-4cff-ab0a-a967a2a68e39"]}}}], "track_and_facet_info": {"experimental_lab": "Tomoko Yamada, NW", "experiment_type": "DNA SPRITE", "experiment_bucket": "Derived cluster files provided by the Yamada Lab and a 4DN-DCIC generated mcool file for visualization", "dataset": "SPRITE on mouse cerebellar tissue", "condition": "PND 22", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cerebellum - PND 22", "lab_name": "4DN DCIC, HMS", "track_title": "contact matrix for cerebellum - PND 22 DNA SPRITE"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-05-24T15:58:58.639031+00:00"}}, {"genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIW7KQ5YP.clusters.gz", "accession": "4DNFIW7KQ5YP", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/567df72d-143d-4421-a19c-a11f9c8d7e33/4DNFIW7KQ5YP.clusters.gz", "uuid": "567df72d-143d-4421-a19c-a11f9c8d7e33", "@id": "/files-processed/4DNFIW7KQ5YP/", "status": "released", "file_size": 4007700145, "href": "/files-processed/4DNFIW7KQ5YP/@@download/4DNFIW7KQ5YP.clusters.gz", "file_type_detailed": "multi-contact read clusters (clusters)", "file_type": "multi-contact read clusters", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "e4696bdd-7a8f-44ee-ad69-1502061c5cf1", "file_format": "clusters", "@id": "/file-formats/clusters/", "display_title": "clusters", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Tomoko Yamada, NW", "experiment_type": "DNA SPRITE", "experiment_bucket": "Derived cluster files provided by the Yamada Lab and a 4DN-DCIC generated mcool file for visualization", "dataset": "SPRITE on mouse cerebellar tissue", "condition": "PND 22", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cerebellum - PND 22", "lab_name": "Tomoko Yamada, NW"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-05-24T16:00:58.532034+00:00"}}, {"genome_assembly": "GRCm38", "@type": ["FileProcessed", "File", "Item"], "display_title": "4DNFIZERUF7M.clusters.gz", "accession": "4DNFIZERUF7M", "open_data_url": "https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/6ea8e8d2-36ed-4695-b2f3-98ca8dad987d/4DNFIZERUF7M.clusters.gz", "uuid": "6ea8e8d2-36ed-4695-b2f3-98ca8dad987d", "@id": "/files-processed/4DNFIZERUF7M/", "status": "released", "file_size": 640396109, "href": "/files-processed/4DNFIZERUF7M/@@download/4DNFIZERUF7M.clusters.gz", "file_type_detailed": "multi-contact read clusters (clusters)", "file_type": "multi-contact read clusters", "file_format": {"status": "released", "@type": ["FileFormat", "Item"], "uuid": "e4696bdd-7a8f-44ee-ad69-1502061c5cf1", "file_format": "clusters", "@id": "/file-formats/clusters/", "display_title": "clusters", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "track_and_facet_info": {"experimental_lab": "Tomoko Yamada, NW", "experiment_type": "DNA SPRITE", "experiment_bucket": "Derived cluster files provided by the Yamada Lab and a 4DN-DCIC generated mcool file for visualization", "dataset": "SPRITE on mouse cerebellar tissue", "condition": "PND 22", "replicate_info": "Biorep 1, Techrep 1", "biosource_name": "cerebellum - PND 22", "lab_name": "Tomoko Yamada, NW"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "last_modified": {"date_modified": "2024-05-24T16:00:14.041195+00:00"}}], "title": "Derived cluster files provided by the Yamada Lab and a 4DN-DCIC generated mcool file for visualization", "description": "The provided cluster files are provided for each biological replicate and have been filtered and processed using the Guttman lab SPRITE processing pipeline as described in the experimental protocol and available here: https://github.com/GuttmanLab/sprite-pipeline/wiki. The mcool matrix file was generated at the 4DN-DCIC using cooler version 0.8.11, scripts based on this gist: https://gist.github.com/nvictus/aacf3530b95251e1a0945a7e36fa28ac and the zoomify function."}], "library_preparation_date": "2020-08-18", "fragment_size_selection_method": "SPRI beads", "@id": "/experiments-seq/4DNEX2BYUC69/", "@type": ["ExperimentSeq", "Experiment", "Item"], "uuid": "9556bcc3-f596-45e8-8480-42c653c7e144", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "DNA SPRITE on cerebellum - PND 22 - 4DNEX2BYUC69", "external_references": [], "experiment_sets": [{"status": "released", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES48PQH94/", "uuid": "768b97bd-214e-4a18-86f7-fcb3aaa5eab5", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES48PQH94", "accession": "4DNES48PQH94", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"journal": "bioRxiv : the preprint server for biology", "status": "current", "authors": ["Zhao Z", "Parra OP", "Musella F", "Scrutton-Alvarado N", "Fujita SI", "Alber F", "Yang Y", "Yamada T"], "@id": "/publications/dee249a4-3f69-4a9e-b7e2-51c643b449a3/", "ID": "doi:10.1101/2023.07.19.549737", "short_attribution": "Zhao Z et al. (2023)", "title": "Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum.", "uuid": "dee249a4-3f69-4a9e-b7e2-51c643b449a3", "@type": ["Publication", "Item"], "display_title": "Zhao Z et al. (2023) doi:10.1101/2023.07.19.549737", "abstract": "Dynamic regulation of gene expression plays a key role in establishing the  diverse neuronal cell types in the brain. Recent findings in genome biology  suggest that three-dimensional (3D) genome organization has important, but  mechanistically poorly understood functions in gene transcription. Beyond local  genomic interactions between promoters and enhancers, we find that cerebellar  granule neurons undergoing differentiation in vivo exhibit striking increases in  long-distance genomic interactions between transcriptionally active genomic loci,  which are separated by tens of megabases within a chromosome or located on  different chromosomes. Among these interactions, we identify a nuclear  subcompartment enriched for near-megabase long enhancers and their associated  neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes  are differentially recruited to this enhancer-dense subcompartment to help shape  the transcriptional identities of granule neuron subtypes in the cerebellum.  SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D  genome modeling and imaging approaches, reveal that the enhancer-dense  subcompartment forms prominent nuclear structures, which we term mega-enhancer  bodies. These novel nuclear bodies reside in the nuclear periphery, away from  other transcriptionally active structures, including nuclear speckles located in  the nuclear interior. Together, our findings define additional layers of  higher-order 3D genome organization closely linked to neuronal maturation and  identity in the brain.", "date_published": "2023-07-25", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"authors": ["Zhao Z", "Parra OP", "Musella F", "Scrutton-Alvarado N", "Fujita SI", "Alber F", "Yang Y", "Yamada T"], "ID": "doi:10.1101/2023.07.19.549737", "display_title": "Zhao Z et al. (2023) doi:10.1101/2023.07.19.549737", "date_published": "2023-07-25", "journal": "bioRxiv : the preprint server for biology", "@id": "/publications/dee249a4-3f69-4a9e-b7e2-51c643b449a3/", "status": "current", "abstract": "Dynamic regulation of gene expression plays a key role in establishing the  diverse neuronal cell types in the brain. Recent findings in genome biology  suggest that three-dimensional (3D) genome organization has important, but  mechanistically poorly understood functions in gene transcription. Beyond local  genomic interactions between promoters and enhancers, we find that cerebellar  granule neurons undergoing differentiation in vivo exhibit striking increases in  long-distance genomic interactions between transcriptionally active genomic loci,  which are separated by tens of megabases within a chromosome or located on  different chromosomes. Among these interactions, we identify a nuclear  subcompartment enriched for near-megabase long enhancers and their associated  neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes  are differentially recruited to this enhancer-dense subcompartment to help shape  the transcriptional identities of granule neuron subtypes in the cerebellum.  SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D  genome modeling and imaging approaches, reveal that the enhancer-dense  subcompartment forms prominent nuclear structures, which we term mega-enhancer  bodies. These novel nuclear bodies reside in the nuclear periphery, away from  other transcriptionally active structures, including nuclear speckles located in  the nuclear interior. Together, our findings define additional layers of  higher-order 3D genome organization closely linked to neuronal maturation and  identity in the brain.", "@type": ["Publication", "Item"], "short_attribution": "Zhao Z et al. (2023)", "uuid": "dee249a4-3f69-4a9e-b7e2-51c643b449a3", "title": "Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Default", "value": null}, "experiment_summary": "DNA SPRITE on cerebellum - PND 22", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}