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"cc6d66d5-ea89-4e9e-9e88-5c310bafa308", "url": "https://s3.amazonaws.com/elasticbeanstalk-fourfront-webprod-wfoutput/4DNFIJVTA2E6/pairsqc_report.html", "@id": "/quality-metrics-pairsqc/cc6d66d5-ea89-4e9e-9e88-5c310bafa308/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "quality_metric_summary": [{"title": "Filtered Reads", "value": "273199491", "numberType": "integer"}, {"title": "Cis reads (>20kb)", "value": "57.538", "tooltip": "Percent of filtered reads (=157.19m)", "numberType": "percent"}, {"title": "Short cis reads", "value": "25.969", "tooltip": "Percent of filtered reads (=70.95m)", "numberType": "percent"}, {"title": "Trans Reads", "value": "16.493", "tooltip": "Percent of filtered reads (=45.06m)", "numberType": "percent"}]}, "track_and_facet_info": {"experimental_lab": "David Zarkower, UMN", "experiment_type": "in situ Hi-C", "experiment_bucket": "HiC Processing Pipeline - v0.3.0", "assay_info": "Arima - A1, A2", "dataset": "Hi-C on mouse somatic gonadal cells", "condition": "female granulosa cells", "replicate_info": "Biorep 2, Techrep 1", "biosource_name": "granulosa cell", "lab_name": "4DN DCIC, HMS"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "file_format": {"@type": ["FileFormat", "Item"], "display_title": "pairs", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b2c", "file_format": "pairs", "@id": "/file-formats/pairs/", "status": "released", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "last_modified": {"date_modified": "2024-08-08T02:01:45.206713+00:00"}}], "title": "HiC Processing Pipeline - v0.3.0", "description": "These are files generated using the updated Hi-C processing pipeline. They should be largely similar to those available in the Processed Files tab, which were generated with the previous version of the standard pipeline.  One potential difference of note is that the version of cooler used to generate the mcool file has a bug fix to prevent a pixel duplication issue which is observed in some files generated by the previous version of the pipeline.  Another notable difference is that a filter is applied to remove reads with MAPQ scores below 30 prior to mcool file generation."}], "biosample_quantity_units": "cells", "crosslinking_temperature": 25.0, "library_preparation_date": "2019-08-29", "fragment_size_selection_method": "gel", "@id": "/experiments-hi-c/4DNEXDK2R8M5/", "@type": ["ExperimentHiC", "Experiment", "Item"], "uuid": "c3079199-28c2-414c-b634-950cc0e02c9e", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "in situ Hi-C on granulosa cell with Arima - A1, A2 - 4DNEXDK2R8M5", "external_references": [{"ref": "GEO:GSM5184266", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5184266"}, {"ref": "SRA:SRX10404229", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRX10404229"}], "experiment_sets": [{"experimentset_type": "replicate", "status": "released", "@id": "/experiment-set-replicates/4DNESSS7VU57/", "accession": "4DNESSS7VU57", "uuid": "5095abf6-03f4-49ec-a1db-0661493b30a8", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNESSS7VU57", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"authors": ["Lindeman RE", "Murphy MW", "Agrimson KS", "Gewiss RL", "Bardwell VJ", "Gearhart MD", "Zarkower D"], "short_attribution": "Lindeman RE et al. (2021)", "status": "current", "uuid": "9a3e1015-b41e-4bdc-8eea-419f536815ec", "@type": ["Publication", "Item"], "ID": "PMID:34096593", "display_title": "Lindeman RE et al. (2021) PMID:34096593", "abstract": "Mammalian sexual development commences when fetal bipotential progenitor cells adopt male Sertoli (in XY) or female granulosa (in XX) gonadal cell fates. Differentiation of these cells involves extensive divergence in chromatin state and gene expression, reflecting distinct roles in sexual differentiation and gametogenesis. Surprisingly, differentiated gonadal cell fates require active maintenance through postnatal life to prevent sexual transdifferentiation and female cell fate can be reprogrammed by ectopic expression of the sex regulator DMRT1. Here we examine how DMRT1 reprograms granulosa cells to Sertoli-like cells in vivo and in culture. We define postnatal sex-biased gene expression programs and identify three-dimensional chromatin contacts and differentially accessible chromatin regions (DARs) associated with differentially expressed genes. Using a  conditional transgene we find DMRT1 only partially reprograms the ovarian transcriptome in the absence of SOX9 and its paralog SOX8, indicating that these  factors functionally cooperate with DMRT1. ATAC-seq and ChIP-seq show that DMRT1  induces formation of many DARs that it binds with SOX9, and DMRT1 is required for binding of SOX9 at most of these. We suggest that DMRT1 can act as a pioneer factor to open chromatin and allow binding of SOX9, which then cooperates with DMRT1 to reprogram sexual cell fate.", "title": "The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming.", "journal": "Nucleic acids research", "@id": "/publications/9a3e1015-b41e-4bdc-8eea-419f536815ec/", "date_published": "2021-06-07", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"abstract": "Mammalian sexual development commences when fetal bipotential progenitor cells adopt male Sertoli (in XY) or female granulosa (in XX) gonadal cell fates. Differentiation of these cells involves extensive divergence in chromatin state and gene expression, reflecting distinct roles in sexual differentiation and gametogenesis. Surprisingly, differentiated gonadal cell fates require active maintenance through postnatal life to prevent sexual transdifferentiation and female cell fate can be reprogrammed by ectopic expression of the sex regulator DMRT1. Here we examine how DMRT1 reprograms granulosa cells to Sertoli-like cells in vivo and in culture. We define postnatal sex-biased gene expression programs and identify three-dimensional chromatin contacts and differentially accessible chromatin regions (DARs) associated with differentially expressed genes. Using a  conditional transgene we find DMRT1 only partially reprograms the ovarian transcriptome in the absence of SOX9 and its paralog SOX8, indicating that these  factors functionally cooperate with DMRT1. ATAC-seq and ChIP-seq show that DMRT1  induces formation of many DARs that it binds with SOX9, and DMRT1 is required for binding of SOX9 at most of these. We suggest that DMRT1 can act as a pioneer factor to open chromatin and allow binding of SOX9, which then cooperates with DMRT1 to reprogram sexual cell fate.", "@type": ["Publication", "Item"], "ID": "PMID:34096593", "authors": ["Lindeman RE", "Murphy MW", "Agrimson KS", "Gewiss RL", "Bardwell VJ", "Gearhart MD", "Zarkower D"], "@id": "/publications/9a3e1015-b41e-4bdc-8eea-419f536815ec/", "short_attribution": "Lindeman RE et al. (2021)", "display_title": "Lindeman RE et al. (2021) PMID:34096593", "title": "The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming.", "status": "current", "uuid": "9a3e1015-b41e-4bdc-8eea-419f536815ec", "date_published": "2021-06-07", "journal": "Nucleic acids research", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Enzyme", "value": "Arima - A1, A2", "combined": "Enzyme: Arima - A1, A2"}, "experiment_summary": "in situ Hi-C on granulosa cell with Arima - A1, A2", "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}