{"@context": "/terms/", "@id": "/search/?type=FileSet", "@type": ["FileSetSearchResults", "ItemSearchResults", "Search"], "title": "Search", "filters": [{"field": "type", "term": "FileSet", "remove": "/search/?"}], "facets": [{"field": "type", "title": "Data Type", "total": 0, "hide_from_view": true, "aggregation_type": "terms", "terms": [{"key": "FileSet", "doc_count": 581}, {"key": "Item", "doc_count": 581}], "original_terms": [{"key": "FileSet", "doc_count": 581}, {"key": "Item", "doc_count": 581}], "extra_aggs": {"meta": {}, "requested_agg": {"doc_count_error_upper_bound": 0, "sum_other_doc_count": 0, "buckets": [{"key": "FileSet", "doc_count": 581}, {"key": "Item", "doc_count": 581}]}}}, {"field": "submission_centers.display_title", "title": "Submitted By", "total": 0, "grouping": "Mergeable Files", "extended_description": "<p>The Mergeable Files grouping can help guide whether certain files within file sets are candidates for merging. Submitted by data can always be searched on, but if additional facets for sample source, sequencing and assay are available, this indicates there are file sets that contain files that could potentially be merged with others. File sets that match values across all 4 fields: Submitted By, Sample Source Tag, Sequencing Tag and Assay Tag are candidates for merge. </p>", "aggregation_type": "terms", "terms": [{"key": "BCM GCC", "doc_count": 128}, {"key": "UWSC GCC", "doc_count": 104}, {"key": "BCH2 TTD", "doc_count": 93}, {"key": "BROAD GCC", "doc_count": 92}, {"key": "WASHU GCC", "doc_count": 91}, {"key": "NYGC GCC", "doc_count": 34}, {"key": "BCM1 TTD", "doc_count": 24}, {"key": "UMICH TTD", "doc_count": 14}, {"key": "NYU TTD", "doc_count": 1}], "original_terms": [{"key": "BCM GCC", "doc_count": 128}, {"key": "UWSC GCC", "doc_count": 104}, {"key": "BCH2 TTD", "doc_count": 93}, {"key": "BROAD GCC", "doc_count": 92}, {"key": "WASHU GCC", "doc_count": 91}, {"key": "NYGC GCC", "doc_count": 34}, {"key": "BCM1 TTD", "doc_count": 24}, {"key": "UMICH TTD", "doc_count": 14}, {"key": "NYU TTD", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "file_group.sample_source", "title": "Sample Source Tag", "total": 0, "grouping": "Mergeable Files", "aggregation_type": "terms", "terms": [{"key": "No value", "doc_count": 178}, {"key": "UWSC_CELL-CULTURE-MIXTURE_COLO829BLT_50_TO_1", "doc_count": 45}, {"key": "NDRI_TISSUE_ST001-1D_LUNG", "doc_count": 43}, {"key": "NDRI_TISSUE_ST002-1D_LUNG", "doc_count": 43}, {"key": "NDRI_TISSUE_ST001-1A_LIVER", "doc_count": 39}, {"key": "NDRI_TISSUE_ST002-1G_COLON", "doc_count": 38}, {"key": "NDRI_TISSUE_ST003-1Q_BRAIN", "doc_count": 35}, {"key": "NDRI_TISSUE_ST004-1Q_BRAIN", "doc_count": 35}, {"key": "WASHU_CELL-CULTURE-MIXTURE_SMAHT_CORIELL_POOL1", "doc_count": 35}, {"key": "UWSC_CELL-CULTURE_COLO-829BL_1", "doc_count": 33}, {"key": "MAYO_CELL-CULTURE_LB_LA2", "doc_count": 30}, {"key": "UWSC_CELL-CULTURE_COLO-829T_2", "doc_count": 12}, {"key": "MAYO_CELL-CULTURE_LB_LA2_2", "doc_count": 3}, {"key": "MAYO_CELL-CULTURE_LB_LA2_60", "doc_count": 3}, {"key": "NDRI_TISSUE_ST001-1K_SKIN", "doc_count": 3}, {"key": "NDRI_TISSUE_ST002-1K_SKIN", "doc_count": 3}, {"key": "MAYO_CELL-CULTURE_LB_LA2_1", "doc_count": 1}, {"key": "MAYO_CELL-CULTURE_LB_LA2_4", "doc_count": 1}, {"key": "MAYO_CELL-CULTURE_LB_LA2_52", "doc_count": 1}], "original_terms": [{"key": "No value", "doc_count": 178}, {"key": "UWSC_CELL-CULTURE-MIXTURE_COLO829BLT_50_TO_1", "doc_count": 45}, {"key": "NDRI_TISSUE_ST001-1D_LUNG", "doc_count": 43}, {"key": "NDRI_TISSUE_ST002-1D_LUNG", "doc_count": 43}, {"key": "NDRI_TISSUE_ST001-1A_LIVER", "doc_count": 39}, {"key": "NDRI_TISSUE_ST002-1G_COLON", "doc_count": 38}, {"key": "NDRI_TISSUE_ST003-1Q_BRAIN", "doc_count": 35}, {"key": "NDRI_TISSUE_ST004-1Q_BRAIN", "doc_count": 35}, {"key": "WASHU_CELL-CULTURE-MIXTURE_SMAHT_CORIELL_POOL1", "doc_count": 35}, {"key": "UWSC_CELL-CULTURE_COLO-829BL_1", "doc_count": 33}, {"key": "MAYO_CELL-CULTURE_LB_LA2", "doc_count": 30}, {"key": "UWSC_CELL-CULTURE_COLO-829T_2", "doc_count": 12}, {"key": "MAYO_CELL-CULTURE_LB_LA2_2", "doc_count": 3}, {"key": "MAYO_CELL-CULTURE_LB_LA2_60", "doc_count": 3}, {"key": "NDRI_TISSUE_ST001-1K_SKIN", "doc_count": 3}, {"key": "NDRI_TISSUE_ST002-1K_SKIN", "doc_count": 3}, {"key": "MAYO_CELL-CULTURE_LB_LA2_1", "doc_count": 1}, {"key": "MAYO_CELL-CULTURE_LB_LA2_4", "doc_count": 1}, {"key": "MAYO_CELL-CULTURE_LB_LA2_52", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "file_group.sequencing", "title": "Sequencing Tag", "total": 0, "grouping": "Mergeable Files", "aggregation_type": "terms", "terms": [{"key": "No value", "doc_count": 178}, {"key": "illumina_novaseq_x_plus-Paired-end-150-25B", "doc_count": 113}, {"key": "illumina_novaseq_x_plus-Paired-end-150-no-flow-cell", "doc_count": 45}, {"key": "illumina_novaseq_x_plus-Paired-end-150-10B", "doc_count": 39}, {"key": "illumina_novaseq_6000-Paired-end-150-S4", "doc_count": 32}, {"key": "pacbio_revio_hifi-Single-end-20000-no-flow-cell", "doc_count": 31}, {"key": "ont_promethion_24-Single-end-27500-R10.4.1", "doc_count": 27}, {"key": "pacbio_revio_hifi-Single-end-17500-no-flow-cell", "doc_count": 18}, {"key": "pacbio_revio_hifi-Single-end-20000-SMRT Cell 25M", "doc_count": 14}, {"key": "ont_promethion_24-Single-end-50000-R10.4.1", "doc_count": 10}, {"key": "illumina_novaseq_x-Paired-end-150-no-flow-cell", "doc_count": 9}, {"key": "illumina_novaseq_x_plus-Paired-end-99-25B", "doc_count": 9}, {"key": "ont_promethion_24-Single-end-15000-R10.4.1", "doc_count": 9}, {"key": "pacbio_revio_hifi-Single-end-2000-no-flow-cell", "doc_count": 9}, {"key": "illumina_novaseq_x_plus-Paired-end-145-25B", "doc_count": 7}, {"key": "pacbio_revio_hifi-Single-end-15000-no-flow-cell", "doc_count": 4}, {"key": "ont_promethion_24-Single-end-100000-R10", "doc_count": 2}, {"key": "ont_promethion_24-Single-end-100000-R9", "doc_count": 2}, {"key": "pacbio_revio_hifi-Single-end-16000-no-flow-cell", "doc_count": 2}, {"key": "illumina_novaseq_6000-Paired-end-150-SP", "doc_count": 1}, {"key": "illumina_novaseq_6000-Paired-end-150-no-flow-cell", "doc_count": 1}, {"key": "illumina_novaseq_x_plus-Paired-end-145-10B", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R10", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R9", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R9.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-13000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1400-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1600-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1800-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-20000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-2100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-2300-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-3000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-3100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-36000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-4100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-4300-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-6000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-8900-R10.4.1", "doc_count": 1}, {"key": "pacbio_sequel_iie-Not Applicable-1500-8M", "doc_count": 1}], "original_terms": [{"key": "No value", "doc_count": 178}, {"key": "illumina_novaseq_x_plus-Paired-end-150-25B", "doc_count": 113}, {"key": "illumina_novaseq_x_plus-Paired-end-150-no-flow-cell", "doc_count": 45}, {"key": "illumina_novaseq_x_plus-Paired-end-150-10B", "doc_count": 39}, {"key": "illumina_novaseq_6000-Paired-end-150-S4", "doc_count": 32}, {"key": "pacbio_revio_hifi-Single-end-20000-no-flow-cell", "doc_count": 31}, {"key": "ont_promethion_24-Single-end-27500-R10.4.1", "doc_count": 27}, {"key": "pacbio_revio_hifi-Single-end-17500-no-flow-cell", "doc_count": 18}, {"key": "pacbio_revio_hifi-Single-end-20000-SMRT Cell 25M", "doc_count": 14}, {"key": "ont_promethion_24-Single-end-50000-R10.4.1", "doc_count": 10}, {"key": "illumina_novaseq_x-Paired-end-150-no-flow-cell", "doc_count": 9}, {"key": "illumina_novaseq_x_plus-Paired-end-99-25B", "doc_count": 9}, {"key": "ont_promethion_24-Single-end-15000-R10.4.1", "doc_count": 9}, {"key": "pacbio_revio_hifi-Single-end-2000-no-flow-cell", "doc_count": 9}, {"key": "illumina_novaseq_x_plus-Paired-end-145-25B", "doc_count": 7}, {"key": "pacbio_revio_hifi-Single-end-15000-no-flow-cell", "doc_count": 4}, {"key": "ont_promethion_24-Single-end-100000-R10", "doc_count": 2}, {"key": "ont_promethion_24-Single-end-100000-R9", "doc_count": 2}, {"key": "pacbio_revio_hifi-Single-end-16000-no-flow-cell", "doc_count": 2}, {"key": "illumina_novaseq_6000-Paired-end-150-SP", "doc_count": 1}, {"key": "illumina_novaseq_6000-Paired-end-150-no-flow-cell", "doc_count": 1}, {"key": "illumina_novaseq_x_plus-Paired-end-145-10B", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R10", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R9", "doc_count": 1}, {"key": "ont_promethion_24-Single-end-50000-R9.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-13000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1400-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1600-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-1800-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-20000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-2100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-2300-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-3000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-3100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-36000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-4100-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-4300-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-6000-R10.4.1", "doc_count": 1}, {"key": "ont_promethion_2_solo-Single-end-8900-R10.4.1", "doc_count": 1}, {"key": "pacbio_sequel_iie-Not Applicable-1500-8M", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "file_group.assay", "title": "Assay Tag", "total": 0, "grouping": "Mergeable Files", "aggregation_type": "terms", "terms": [{"key": "bulk_wgs_pcr_free", "doc_count": 257}, {"key": "No value", "doc_count": 178}, {"key": "bulk_rna_seq", "doc_count": 45}, {"key": "codec", "doc_count": 21}, {"key": "bulk_fiberseq", "doc_count": 16}, {"key": "nanoseq", "doc_count": 14}, {"key": "tencats", "doc_count": 14}, {"key": "bulk_mas_iso_seq", "doc_count": 11}, {"key": "compduplex_seq", "doc_count": 10}, {"key": "vista_seq", "doc_count": 9}, {"key": "bulk_ultralong_wgs", "doc_count": 4}, {"key": "bulk_hic", "doc_count": 1}, {"key": "hidef_seq", "doc_count": 1}], "original_terms": [{"key": "bulk_wgs_pcr_free", "doc_count": 257}, {"key": "No value", "doc_count": 178}, {"key": "bulk_rna_seq", "doc_count": 45}, {"key": "codec", "doc_count": 21}, {"key": "bulk_fiberseq", "doc_count": 16}, {"key": "nanoseq", "doc_count": 14}, {"key": "tencats", "doc_count": 14}, {"key": "bulk_mas_iso_seq", "doc_count": 11}, {"key": "compduplex_seq", "doc_count": 10}, {"key": "vista_seq", "doc_count": 9}, {"key": "bulk_ultralong_wgs", "doc_count": 4}, {"key": "bulk_hic", "doc_count": 1}, {"key": "hidef_seq", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "file_group.group_tag", "title": "Group Tag", "total": 0, "grouping": "Mergeable Files", "aggregation_type": "terms", "terms": [{"key": "", "doc_count": 393}, {"key": "No value", "doc_count": 178}, {"key": "group1", "doc_count": 10}], "original_terms": [{"key": "", "doc_count": 393}, {"key": "No value", "doc_count": 178}, {"key": "group1", "doc_count": 10}], "extra_aggs": {"meta": {}}}, {"field": "libraries.assay.display_title", "title": "Assay", "total": 0, "aggregation_type": "terms", "terms": [{"key": "WGS", "doc_count": 257}, {"key": "Single-cell PTA WGS", "doc_count": 94}, {"key": "scVISTA-seq", "doc_count": 84}, {"key": "RNA-seq", "doc_count": 45}, {"key": "CODEC", "doc_count": 21}, {"key": "Fiber-seq", "doc_count": 16}, {"key": "NanoSeq", "doc_count": 14}, {"key": "TEnCATS", "doc_count": 14}, {"key": "Kinnex", "doc_count": 11}, {"key": "CompDuplex-seq", "doc_count": 10}, {"key": "VISTA-seq", "doc_count": 9}, {"key": "Ultra-Long WGS", "doc_count": 4}, {"key": "Hi-C", "doc_count": 1}, {"key": "HiDEF-seq", "doc_count": 1}], "original_terms": [{"key": "WGS", "doc_count": 257}, {"key": "Single-cell PTA WGS", "doc_count": 94}, {"key": "scVISTA-seq", "doc_count": 84}, {"key": "RNA-seq", "doc_count": 45}, {"key": "CODEC", "doc_count": 21}, {"key": "Fiber-seq", "doc_count": 16}, {"key": "NanoSeq", "doc_count": 14}, {"key": "TEnCATS", "doc_count": 14}, {"key": "Kinnex", "doc_count": 11}, {"key": "CompDuplex-seq", "doc_count": 10}, {"key": "VISTA-seq", "doc_count": 9}, {"key": "Ultra-Long WGS", "doc_count": 4}, {"key": "Hi-C", "doc_count": 1}, {"key": "HiDEF-seq", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "sequencing.sequencer.display_title", "title": "Sequencer", "total": 0, "aggregation_type": "terms", "terms": [{"key": "Illumina NovaSeq X Plus", "doc_count": 308}, {"key": "Illumina NovaSeq X", "doc_count": 93}, {"key": "PacBio Revio", "doc_count": 78}, {"key": "ONT PromethION 24", "doc_count": 53}, {"key": "Illumina NovaSeq 6000", "doc_count": 34}, {"key": "ONT PromethION 2 Solo", "doc_count": 14}, {"key": "PacBio Sequel IIe", "doc_count": 1}], "original_terms": [{"key": "Illumina NovaSeq X Plus", "doc_count": 308}, {"key": "Illumina NovaSeq X", "doc_count": 93}, {"key": "PacBio Revio", "doc_count": 78}, {"key": "ONT PromethION 24", "doc_count": 53}, {"key": "Illumina NovaSeq 6000", "doc_count": 34}, {"key": "ONT PromethION 2 Solo", "doc_count": 14}, {"key": "PacBio Sequel IIe", "doc_count": 1}], "extra_aggs": {"meta": {}}}, {"field": "status", "title": "Status", "total": 0, "aggregation_type": "terms", "terms": [{"key": "open", "doc_count": 581}], "original_terms": [{"key": "open", "doc_count": 581}], "extra_aggs": {"meta": {}}}], "@graph": [{"tissue_types": ["Brain"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:05.192389+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST004-BRAIN_ONT.P2_ALU.CAPTURE", "libraries": [{"dna_target": ["AluY5a", "AluY8"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-103X_BRAIN", "accession": "SMAANPXRSQIX", "@id": "/analytes/c36f1647-042f-4165-bf65-c9e258b39772/", "uuid": "c36f1647-042f-4165-bf65-c9e258b39772", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "accession": "SMADOKPHCXLL", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-103X", "accession": "SMATSU1OHDQ7", "@id": "/tissue-samples/a6974e28-d353-44bc-9f06-314b3dcbe07c/", "uuid": "a6974e28-d353-44bc-9f06-314b3dcbe07c", "status": "open"}], "status": "open"}, {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-104X_BRAIN", "accession": "SMAANKQY3X6O", "@id": "/analytes/893f2c08-2f3c-4d9d-ab5c-6b4f9758e1b0/", "uuid": "893f2c08-2f3c-4d9d-ab5c-6b4f9758e1b0", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "accession": "SMADOKPHCXLL", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-104X", "accession": "SMATSI7XVGXG", "@id": "/tissue-samples/30c6dc1e-61a5-4611-9cd4-d1272c96a756/", "uuid": "30c6dc1e-61a5-4611-9cd4-d1272c96a756", "status": "open"}], "status": "open"}, {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-105X_BRAIN", "accession": "SMAANUN1XTFZ", "@id": "/analytes/af0b3506-e8e0-477a-af49-45156bd449af/", "uuid": "af0b3506-e8e0-477a-af49-45156bd449af", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "accession": "SMADOKPHCXLL", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-105X", "accession": "SMATS72EDO23", "@id": "/tissue-samples/4078eadc-4d73-4c9a-a966-e701318d7dba/", "uuid": "4078eadc-4d73-4c9a-a966-e701318d7dba", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CCAGGCTGGAGTGCAGTGGC", "CGCCACTGCAGTCCGCAGTC"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST004-BRAIN_ONT.P2_ALU.CAPTURE", "@id": "/libraries/0b4eae66-7da0-4840-87dc-9d48ac3661cd/", "uuid": "0b4eae66-7da0-4840-87dc-9d48ac3661cd", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["LibraryPreparation", "Preparation", "Item"], "adapter_inclusion_method": ["Ligation"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "strand": "Unstranded", "amplification_method": ["Not Applicable"], "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSX1O44I3", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST004-BRAIN_ONT.P2_ALU.CAPTURE", "uuid": "de5f212b-ff48-4de6-aca3-005bf05e49e2", "tags": ["ready_to_release"], "sequencing": {"target_coverage": 189.0, "read_type": "Single-end", "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST004-BRAIN_ONT.P2_ALU.CAPTURE", "on_target_rate": 0.6844, "submitted_id": "UMICH_SEQUENCING_ST004-BRAIN_ONT.P2_ALU.CAPTURE", "uuid": "c13e7e24-8fc3-4be2-9465-84bff849a635", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 1600, "@id": "/Sequencing/c13e7e24-8fc3-4be2-9465-84bff849a635/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "7395e3e1-4429-432c-ab58-2f6f82b7f52a/SMAARYKLYD7N.bam", "display_title": "ST004-1Q-XX-M73-E028-umich-SMAARYKLYD7N-minimap2_2.26_GRCh38.aligned.sorted.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:22:46.663566+00:00", "uploaded": "2025-11-06T02:29:14.170655+00:00", "uploading": "2025-10-06T20:39:17.096277+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:22:46.663566+00:00", "public_release": "2026-01-30T17:22:46.663566+00:00"}}, "@id": "/aligned-reads/7395e3e1-4429-432c-ab58-2f6f82b7f52a/", "accession": "SMAARYKLYD7N", "uuid": "7395e3e1-4429-432c-ab58-2f6f82b7f52a", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST004-1Q_BRAIN", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-1600-R10.4.1"}, "@id": "/file-sets/de5f212b-ff48-4de6-aca3-005bf05e49e2/", "last_modified": {"date_modified": "2026-01-30T17:22:47.264296+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Brain"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:05.043340+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST004-BRAIN_ONT.P2_L1H.CAPTURE", "libraries": [{"dna_target": ["L1H"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-103X_BRAIN", "@id": "/analytes/c36f1647-042f-4165-bf65-c9e258b39772/", "accession": "SMAANPXRSQIX", "uuid": "c36f1647-042f-4165-bf65-c9e258b39772", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "accession": "SMADOKPHCXLL", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-103X", "@id": "/tissue-samples/a6974e28-d353-44bc-9f06-314b3dcbe07c/", "accession": "SMATSU1OHDQ7", "uuid": "a6974e28-d353-44bc-9f06-314b3dcbe07c", "status": "open"}], "status": "open"}, {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-104X_BRAIN", "@id": "/analytes/893f2c08-2f3c-4d9d-ab5c-6b4f9758e1b0/", "accession": "SMAANKQY3X6O", "uuid": "893f2c08-2f3c-4d9d-ab5c-6b4f9758e1b0", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "accession": "SMADOKPHCXLL", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-104X", "@id": "/tissue-samples/30c6dc1e-61a5-4611-9cd4-d1272c96a756/", "accession": "SMATSI7XVGXG", "uuid": "30c6dc1e-61a5-4611-9cd4-d1272c96a756", "status": "open"}], "status": "open"}, {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST004-1Q-105X_BRAIN", "@id": "/analytes/af0b3506-e8e0-477a-af49-45156bd449af/", "accession": "SMAANUN1XTFZ", "uuid": "af0b3506-e8e0-477a-af49-45156bd449af", "samples": [{"sample_sources": [{"code": "ST004-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST004", "@id": "/donors/0222e296-2430-4f74-bd70-4b181ba48eb6/", "accession": "SMADOKPHCXLL", "uuid": "0222e296-2430-4f74-bd70-4b181ba48eb6", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "display_title": "ST004-1Q", "@id": "/tissues/ce6667ea-8115-4273-8bf0-23bde2bc21d2/", "submitted_id": "NDRI_TISSUE_ST004-1Q_BRAIN", "uuid": "ce6667ea-8115-4273-8bf0-23bde2bc21d2", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST004-1Q-105X", "@id": "/tissue-samples/4078eadc-4d73-4c9a-a966-e701318d7dba/", "accession": "SMATS72EDO23", "uuid": "4078eadc-4d73-4c9a-a966-e701318d7dba", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CTAATGTGTCATCTAGCATT"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST004-BRAIN_ONT.P2_L1H.CAPTURE", "@id": "/libraries/5259d567-cac9-4720-a1bd-506dee5b51f9/", "uuid": "5259d567-cac9-4720-a1bd-506dee5b51f9", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "amplification_method": ["Not Applicable"], "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSWCZF4CV", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST004-BRAIN_ONT.P2_L1H.CAPTURE", "uuid": "44737058-99b6-46e8-8cc8-ea15400a8cef", "tags": ["ready_to_release"], "sequencing": {"read_type": "Single-end", "target_coverage": 374.0, "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST004-BRAIN_ONT.P2_L1H.CAPTURE", "on_target_rate": 0.1467, "submitted_id": "UMICH_SEQUENCING_ST004-BRAIN_ONT.P2_L1H.CAPTURE", "uuid": "2b3d257a-cec4-4b23-b4a7-18437fa0df8f", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 1400, "@id": "/Sequencing/2b3d257a-cec4-4b23-b4a7-18437fa0df8f/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "d2e4d480-723a-4672-ae98-a5302cce8f3e/SMAARIXTNE4P.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:23.228241+00:00", "uploaded": "2025-11-06T02:38:17.508788+00:00", "uploading": "2025-10-06T20:39:17.803499+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:23.228241+00:00", "public_release": "2026-01-30T17:26:23.228241+00:00"}}, "display_title": "ST004-1Q-XX-M73-E028-umich-SMAARIXTNE4P-minimap2_2.26_GRCh38.aligned.sorted.bam", "accession": "SMAARIXTNE4P", "@id": "/aligned-reads/d2e4d480-723a-4672-ae98-a5302cce8f3e/", "uuid": "d2e4d480-723a-4672-ae98-a5302cce8f3e", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST004-1Q_BRAIN", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-1400-R10.4.1"}, "@id": "/file-sets/44737058-99b6-46e8-8cc8-ea15400a8cef/", "last_modified": {"date_modified": "2026-01-30T17:26:24.107235+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Brain"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.843966+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST003-BRAIN_ONT.P2_ALU.CAPTURE", "libraries": [{"dna_target": ["AluY5a", "AluY8"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST003-1Q-103X_BRAIN", "@id": "/analytes/2e216399-eed5-4fdc-b626-fc5de0736156/", "accession": "SMAAN1MSQF7A", "uuid": "2e216399-eed5-4fdc-b626-fc5de0736156", "samples": [{"sample_sources": [{"code": "ST003-1Q", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST003", "accession": "SMADOL8DI2SO", "@id": "/donors/fbac0236-ed2d-4855-b323-ba55f2285b0c/", "uuid": "fbac0236-ed2d-4855-b323-ba55f2285b0c", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "display_title": "ST003-1Q", "@id": "/tissues/c0762c4f-b7d6-4d03-8bb6-e49e877fc68e/", "uuid": "c0762c4f-b7d6-4d03-8bb6-e49e877fc68e", "submitted_id": "NDRI_TISSUE_ST003-1Q_BRAIN", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST003-1Q-103X", "accession": "SMATS82JBSKP", "@id": "/tissue-samples/75a42083-f13d-497e-901b-b73702a126a1/", "uuid": "75a42083-f13d-497e-901b-b73702a126a1", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-14", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CCAGGCTGGAGTGCAGTGGC", "CGCCACTGCAGTCCGCAGTC"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST003-BRAIN_ONT.P2_ALU.CAPTURE", "@id": "/libraries/400c3561-dc72-489a-b261-08d0e3634d54/", "uuid": "400c3561-dc72-489a-b261-08d0e3634d54", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "enzymes": ["Cas9"], "description": "Library preparation for TenCATS capture of L1H and Alu elements", "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSTIVFZR9", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST003-BRAIN_ONT.P2_ALU.CAPTURE", "uuid": "60a93887-ad03-4d2d-95df-e021c5afd079", "tags": ["ready_to_release"], "sequencing": {"target_coverage": 251.0, "read_type": "Single-end", "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST003-BRAIN_ONT.P2_ALU.CAPTURE", "on_target_rate": 0.6627, "submitted_id": "UMICH_SEQUENCING_ST003-BRAIN_ONT.P2_ALU.CAPTURE", "uuid": "de281c02-4f89-4ade-8876-acac1f3e349d", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 3000, "@id": "/Sequencing/de281c02-4f89-4ade-8876-acac1f3e349d/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "fbbe3834-cb80-416a-90bb-969539a85837/SMAAR2BKFA9W.bam", "display_title": "ST003-1Q-XX-M22-E028-umich-SMAAR2BKFA9W-minimap2_2.26_GRCh38.aligned.sorted.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:26.194517+00:00", "uploaded": "2025-11-06T02:27:13.452859+00:00", "uploading": "2025-10-06T20:39:14.805462+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:26.194517+00:00", "public_release": "2026-01-30T17:26:26.194517+00:00"}}, "accession": "SMAAR2BKFA9W", "@id": "/aligned-reads/fbbe3834-cb80-416a-90bb-969539a85837/", "uuid": "fbbe3834-cb80-416a-90bb-969539a85837", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST003-1Q_BRAIN", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-3000-R10.4.1"}, "@id": "/file-sets/60a93887-ad03-4d2d-95df-e021c5afd079/", "last_modified": {"date_modified": "2026-01-30T17:26:26.872070+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Brain"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.673027+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST003-BRAIN_ONT.P2_L1H.CAPTURE", "libraries": [{"dna_target": ["L1H"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST003-1Q-103X_BRAIN", "@id": "/analytes/2e216399-eed5-4fdc-b626-fc5de0736156/", "accession": "SMAAN1MSQF7A", "uuid": "2e216399-eed5-4fdc-b626-fc5de0736156", "samples": [{"sample_sources": [{"code": "ST003-1Q", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST003", "@id": "/donors/fbac0236-ed2d-4855-b323-ba55f2285b0c/", "accession": "SMADOL8DI2SO", "uuid": "fbac0236-ed2d-4855-b323-ba55f2285b0c", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "Right Frontal Lobe", "@id": "/ontology-terms/2c4f529d-0f58-4e91-bd5f-b0a5ff03f801/", "uuid": "2c4f529d-0f58-4e91-bd5f-b0a5ff03f801", "status": "open"}, "display_title": "ST003-1Q", "@id": "/tissues/c0762c4f-b7d6-4d03-8bb6-e49e877fc68e/", "submitted_id": "NDRI_TISSUE_ST003-1Q_BRAIN", "uuid": "c0762c4f-b7d6-4d03-8bb6-e49e877fc68e", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST003-1Q-103X", "@id": "/tissue-samples/75a42083-f13d-497e-901b-b73702a126a1/", "accession": "SMATS82JBSKP", "uuid": "75a42083-f13d-497e-901b-b73702a126a1", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-07", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CTAATGTGTCATCTAGCATT"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST003-BRAIN_ONT.P2_L1H.CAPTURE", "@id": "/libraries/3392dd5d-b5da-4c59-b5ef-b487d3abeb76/", "uuid": "3392dd5d-b5da-4c59-b5ef-b487d3abeb76", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["LibraryPreparation", "Preparation", "Item"], "adapter_inclusion_method": ["Ligation"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFS42CTOLM", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST003-BRAIN_ONT.P2_L1H.CAPTURE", "uuid": "dd643267-4d2c-4951-a0cf-f18d55c54e89", "tags": ["ready_to_release"], "sequencing": {"target_coverage": 651.0, "read_type": "Single-end", "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST003-BRAIN_ONT.P2_L1H.CAPTURE", "on_target_rate": 0.2401, "uuid": "29d1e02e-903e-4ba3-8c4c-9f24ec13d4c9", "submitted_id": "UMICH_SEQUENCING_ST003-BRAIN_ONT.P2_L1H.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 2300, "@id": "/Sequencing/29d1e02e-903e-4ba3-8c4c-9f24ec13d4c9/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "12858ba2-329f-45a3-a769-8fea1a8771fb/SMAAR747GROL.bam", "display_title": "ST003-1Q-XX-M22-E028-umich-SMAAR747GROL-minimap2_2.26_GRCh38.aligned.sorted.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:29.676985+00:00", "uploaded": "2025-11-06T02:43:47.786806+00:00", "uploading": "2025-10-06T20:39:16.397556+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:29.676985+00:00", "public_release": "2026-01-30T17:26:29.676985+00:00"}}, "accession": "SMAAR747GROL", "@id": "/aligned-reads/12858ba2-329f-45a3-a769-8fea1a8771fb/", "uuid": "12858ba2-329f-45a3-a769-8fea1a8771fb", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST003-1Q_BRAIN", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-2300-R10.4.1"}, "@id": "/file-sets/dd643267-4d2c-4951-a0cf-f18d55c54e89/", "last_modified": {"date_modified": "2026-01-30T17:26:30.165806+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Colon, Asc"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.528126+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST002-COLON_ONT.P2_ALU.CAPTURE", "libraries": [{"dna_target": ["AluY5a", "AluY8"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST002-1G-103X_COLON", "accession": "SMAANXZZPPUM", "@id": "/analytes/16ed84f3-132e-4d53-9310-c1d4c61dcf57/", "uuid": "16ed84f3-132e-4d53-9310-c1d4c61dcf57", "samples": [{"sample_sources": [{"code": "ST002-1G", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST002", "@id": "/donors/d7163b47-5635-4b07-a2f5-3255f84a5566/", "accession": "SMADO2Y4MMNX", "uuid": "d7163b47-5635-4b07-a2f5-3255f84a5566", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "3E - Colon, Asc", "@id": "/ontology-terms/939990c7-a28e-4d0e-a047-f8684cf7e072/", "uuid": "939990c7-a28e-4d0e-a047-f8684cf7e072", "status": "open"}, "display_title": "ST002-1G", "@id": "/tissues/989d0812-b3fd-45f0-b5bb-dbb435b1bb42/", "uuid": "989d0812-b3fd-45f0-b5bb-dbb435b1bb42", "submitted_id": "NDRI_TISSUE_ST002-1G_COLON", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST002-1G-103X", "accession": "SMATSFR5KGR2", "@id": "/tissue-samples/d07625df-196a-4f42-8df3-88c6b1d54cac/", "uuid": "d07625df-196a-4f42-8df3-88c6b1d54cac", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-21", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CCAGGCTGGAGTGCAGTGGC", "CGCCACTGCAGTCCGCAGTC"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST002-COLON_ONT.P2_ALU.CAPTURE", "@id": "/libraries/5f0b8c1c-8ee0-4745-8cc5-37307383aa03/", "uuid": "5f0b8c1c-8ee0-4745-8cc5-37307383aa03", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "enzymes": ["Cas9"], "description": "Library preparation for TenCATS capture of L1H and Alu elements", "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSEKJ9IV2", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST002-COLON_ONT.P2_ALU.CAPTURE", "uuid": "68d05adb-458b-4eaa-8896-5218ca4a94ab", "tags": ["ready_to_release"], "sequencing": {"target_coverage": 155.0, "read_type": "Single-end", "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST002-COLON_ONT.P2_ALU.CAPTURE", "on_target_rate": 0.4379, "submitted_id": "UMICH_SEQUENCING_ST002-COLON_ONT.P2_ALU.CAPTURE", "uuid": "64eec494-f4be-476d-b966-4cbedbd728ee", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 2100, "@id": "/Sequencing/64eec494-f4be-476d-b966-4cbedbd728ee/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "upload_key": "2ba99ae9-0606-41db-b0ff-c0331d1098b0/SMAARX5IEA9J.bam", "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:33.194294+00:00", "uploaded": "2025-11-06T02:37:05.575592+00:00", "uploading": "2025-10-06T20:39:11.197347+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:33.194294+00:00", "public_release": "2026-01-30T17:26:33.194294+00:00"}}, "display_title": "ST002-1G-XX-M74-E028-umich-SMAARX5IEA9J-minimap2_2.26_GRCh38.aligned.sorted.bam", "@id": "/aligned-reads/2ba99ae9-0606-41db-b0ff-c0331d1098b0/", "accession": "SMAARX5IEA9J", "uuid": "2ba99ae9-0606-41db-b0ff-c0331d1098b0", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST002-1G_COLON", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-2100-R10.4.1"}, "@id": "/file-sets/68d05adb-458b-4eaa-8896-5218ca4a94ab/", "last_modified": {"date_modified": "2026-01-30T17:26:33.778500+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Colon, Asc"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.361449+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST002-COLON_ONT.P2_L1H.CAPTURE", "libraries": [{"dna_target": ["L1H"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST002-1G-103X_COLON", "accession": "SMAANXZZPPUM", "@id": "/analytes/16ed84f3-132e-4d53-9310-c1d4c61dcf57/", "uuid": "16ed84f3-132e-4d53-9310-c1d4c61dcf57", "samples": [{"sample_sources": [{"code": "ST002-1G", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST002", "accession": "SMADO2Y4MMNX", "@id": "/donors/d7163b47-5635-4b07-a2f5-3255f84a5566/", "uuid": "d7163b47-5635-4b07-a2f5-3255f84a5566", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "3E - Colon, Asc", "@id": "/ontology-terms/939990c7-a28e-4d0e-a047-f8684cf7e072/", "uuid": "939990c7-a28e-4d0e-a047-f8684cf7e072", "status": "open"}, "display_title": "ST002-1G", "@id": "/tissues/989d0812-b3fd-45f0-b5bb-dbb435b1bb42/", "uuid": "989d0812-b3fd-45f0-b5bb-dbb435b1bb42", "submitted_id": "NDRI_TISSUE_ST002-1G_COLON", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST002-1G-103X", "@id": "/tissue-samples/d07625df-196a-4f42-8df3-88c6b1d54cac/", "accession": "SMATSFR5KGR2", "uuid": "d07625df-196a-4f42-8df3-88c6b1d54cac", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-06", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CTAATGTGTCATCTAGCATT"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST002-COLON_ONT.P2_L1H.CAPTURE", "@id": "/libraries/59ded25e-cbec-4ba4-ab58-4d27c45c1f85/", "uuid": "59ded25e-cbec-4ba4-ab58-4d27c45c1f85", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["LibraryPreparation", "Preparation", "Item"], "adapter_inclusion_method": ["Ligation"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSTNBVOGY", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST002-COLON_ONT.P2_L1H.CAPTURE", "uuid": "8a3a92fa-3518-48c2-a5db-eaafbd55f68d", "tags": ["ready_to_release"], "sequencing": {"read_type": "Single-end", "target_coverage": 946.0, "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST002-COLON_ONT.P2_L1H.CAPTURE", "on_target_rate": 0.2027, "uuid": "f79bc2f6-587c-43b7-a4d2-c9216bec391d", "submitted_id": "UMICH_SEQUENCING_ST002-COLON_ONT.P2_L1H.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 1800, "@id": "/Sequencing/f79bc2f6-587c-43b7-a4d2-c9216bec391d/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "5f0a7ab9-aff5-4103-b4fb-bee2a6181da2/SMAAR5429TRF.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:36.802161+00:00", "uploaded": "2025-11-06T02:42:52.984399+00:00", "uploading": "2025-10-06T20:39:11.953989+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:36.802161+00:00", "public_release": "2026-01-30T17:26:36.802161+00:00"}}, "display_title": "ST002-1G-XX-M74-E028-umich-SMAAR5429TRF-minimap2_2.26_GRCh38.aligned.sorted.bam", "accession": "SMAAR5429TRF", "@id": "/aligned-reads/5f0a7ab9-aff5-4103-b4fb-bee2a6181da2/", "uuid": "5f0a7ab9-aff5-4103-b4fb-bee2a6181da2", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST002-1G_COLON", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-1800-R10.4.1"}, "@id": "/file-sets/8a3a92fa-3518-48c2-a5db-eaafbd55f68d/", "last_modified": {"date_modified": "2026-01-30T17:26:37.657617+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Lung"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.194034+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST002-LUNG_ONT.P2_ALU.CAPTURE", "libraries": [{"dna_target": ["AluY5a", "AluY8"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST002-1D-103X_LUNG", "accession": "SMAANABIJRQF", "@id": "/analytes/85602c44-31f0-4480-b01d-d383d5056750/", "uuid": "85602c44-31f0-4480-b01d-d383d5056750", "samples": [{"sample_sources": [{"code": "ST002-1D", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST002", "accession": "SMADO2Y4MMNX", "@id": "/donors/d7163b47-5635-4b07-a2f5-3255f84a5566/", "uuid": "d7163b47-5635-4b07-a2f5-3255f84a5566", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Tissue", "SampleSource", "Item"], "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "upper lobe of left lung", "@id": "/ontology-terms/e4489d1f-c640-488a-af3a-02a06a9075a5/", "uuid": "e4489d1f-c640-488a-af3a-02a06a9075a5", "status": "open"}, "display_title": "ST002-1D", "@id": "/tissues/3d829c08-a70b-4202-9e77-5745e14a7272/", "uuid": "3d829c08-a70b-4202-9e77-5745e14a7272", "submitted_id": "NDRI_TISSUE_ST002-1D_LUNG", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST002-1D-103X", "@id": "/tissue-samples/2e607ebc-d622-43e5-99eb-564c6c0e377a/", "accession": "SMATSMBGC2ZE", "uuid": "2e607ebc-d622-43e5-99eb-564c6c0e377a", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-21", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CCAGGCTGGAGTGCAGTGGC", "CGCCACTGCAGTCCGCAGTC"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST002-LUNG_ONT.P2_ALU.CAPTURE", "@id": "/libraries/7a305668-827e-471c-b40d-5188bfab4800/", "uuid": "7a305668-827e-471c-b40d-5188bfab4800", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["LibraryPreparation", "Preparation", "Item"], "adapter_inclusion_method": ["Ligation"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSKONK47F", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST002-LUNG_ONT.P2_ALU.CAPTURE", "uuid": "5f174ab3-39ef-45bb-9e1e-855176045b79", "tags": ["ready_to_release"], "sequencing": {"read_type": "Single-end", "target_coverage": 122.0, "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST002-LUNG_ONT.P2_ALU.CAPTURE", "on_target_rate": 0.5212, "uuid": "6e6aa579-36a9-4b2a-bb09-f1b66ab42ba6", "submitted_id": "UMICH_SEQUENCING_ST002-LUNG_ONT.P2_ALU.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 8900, "@id": "/Sequencing/6e6aa579-36a9-4b2a-bb09-f1b66ab42ba6/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "upload_key": "6432251a-31d9-4a9b-addf-57dabda0ee1f/SMAAR1T9A8A8.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:40.201240+00:00", "uploaded": "2025-11-06T02:44:06.257874+00:00", "uploading": "2025-10-06T20:39:12.615231+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:40.201240+00:00", "public_release": "2026-01-30T17:26:40.201240+00:00"}}, "display_title": "ST002-1D-XX-M74-E028-umich-SMAAR1T9A8A8-minimap2_2.26_GRCh38.aligned.sorted.bam", "accession": "SMAAR1T9A8A8", "@id": "/aligned-reads/6432251a-31d9-4a9b-addf-57dabda0ee1f/", "uuid": "6432251a-31d9-4a9b-addf-57dabda0ee1f", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST002-1D_LUNG", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-8900-R10.4.1"}, "@id": "/file-sets/5f174ab3-39ef-45bb-9e1e-855176045b79/", "last_modified": {"date_modified": "2026-01-30T17:26:40.802441+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Lung"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:04.026412+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST002-LUNG_ONT.P2_L1H.CAPTURE", "libraries": [{"dna_target": ["L1H"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST002-1D-103X_LUNG", "accession": "SMAANABIJRQF", "@id": "/analytes/85602c44-31f0-4480-b01d-d383d5056750/", "uuid": "85602c44-31f0-4480-b01d-d383d5056750", "samples": [{"sample_sources": [{"code": "ST002-1D", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST002", "accession": "SMADO2Y4MMNX", "@id": "/donors/d7163b47-5635-4b07-a2f5-3255f84a5566/", "uuid": "d7163b47-5635-4b07-a2f5-3255f84a5566", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "upper lobe of left lung", "@id": "/ontology-terms/e4489d1f-c640-488a-af3a-02a06a9075a5/", "uuid": "e4489d1f-c640-488a-af3a-02a06a9075a5", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST002-1D", "@id": "/tissues/3d829c08-a70b-4202-9e77-5745e14a7272/", "uuid": "3d829c08-a70b-4202-9e77-5745e14a7272", "submitted_id": "NDRI_TISSUE_ST002-1D_LUNG", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST002-1D-103X", "@id": "/tissue-samples/2e607ebc-d622-43e5-99eb-564c6c0e377a/", "accession": "SMATSMBGC2ZE", "uuid": "2e607ebc-d622-43e5-99eb-564c6c0e377a", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-06", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CTAATGTGTCATCTAGCATT"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST002-LUNG_ONT.P2_L1H.CAPTURE", "@id": "/libraries/68164e34-9a20-4fa7-9a4c-3c7b96779f48/", "uuid": "68164e34-9a20-4fa7-9a4c-3c7b96779f48", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSFHVPSR9", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST002-LUNG_ONT.P2_L1H.CAPTURE", "uuid": "ab5a62ad-7558-4d32-bebb-32316584fbbf", "tags": ["ready_to_release"], "sequencing": {"read_type": "Single-end", "target_coverage": 451.0, "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST002-LUNG_ONT.P2_L1H.CAPTURE", "on_target_rate": 0.2611, "uuid": "a88c60b9-e528-4a9a-ba2c-36f72f49b7e7", "submitted_id": "UMICH_SEQUENCING_ST002-LUNG_ONT.P2_L1H.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 4100, "@id": "/Sequencing/a88c60b9-e528-4a9a-ba2c-36f72f49b7e7/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "upload_key": "42ea4930-cb77-4029-b140-d29bbcc58d59/SMAAR8WKL8S1.bam", "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "display_title": "ST002-1D-XX-M74-E028-umich-SMAAR8WKL8S1-minimap2_2.26_GRCh38.aligned.sorted.bam", "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:44.125684+00:00", "uploaded": "2025-11-06T02:35:34.497090+00:00", "uploading": "2025-10-06T20:39:14.116245+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:44.125684+00:00", "public_release": "2026-01-30T17:26:44.125684+00:00"}}, "accession": "SMAAR8WKL8S1", "@id": "/aligned-reads/42ea4930-cb77-4029-b140-d29bbcc58d59/", "uuid": "42ea4930-cb77-4029-b140-d29bbcc58d59", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST002-1D_LUNG", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-4100-R10.4.1"}, "@id": "/file-sets/ab5a62ad-7558-4d32-bebb-32316584fbbf/", "last_modified": {"date_modified": "2026-01-30T17:26:45.080540+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Liver"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:03.822184+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST001-LIVER_ONT.P2_ALU.CAPTURE", "libraries": [{"dna_target": ["AluY5a", "AluY8"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST001-1A-101X_LIVER", "accession": "SMAAN15PANIC", "@id": "/analytes/f0cad2a2-e42b-4860-ae77-2593ca79e17f/", "uuid": "f0cad2a2-e42b-4860-ae77-2593ca79e17f", "samples": [{"sample_sources": [{"code": "ST001-1A", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST001", "@id": "/donors/3039a6ca-9849-432d-ad49-2c5630bcbee7/", "accession": "SMADOWNO1XMS", "uuid": "3039a6ca-9849-432d-ad49-2c5630bcbee7", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "right lobe of liver", "@id": "/ontology-terms/a68d2524-e527-43b6-bf7d-4e4fd7a9ce8b/", "uuid": "a68d2524-e527-43b6-bf7d-4e4fd7a9ce8b", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST001-1A", "@id": "/tissues/f84d3b01-bef0-46b3-b87a-6542b797730d/", "submitted_id": "NDRI_TISSUE_ST001-1A_LIVER", "uuid": "f84d3b01-bef0-46b3-b87a-6542b797730d", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST001-1A-101X", "@id": "/tissue-samples/2acd0a3d-3bb1-4f45-9f03-2123b498c3bc/", "accession": "SMATSGWX1T9D", "uuid": "2acd0a3d-3bb1-4f45-9f03-2123b498c3bc", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-20", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CCAGGCTGGAGTGCAGTGGC", "CGCCACTGCAGTCCGCAGTC"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST001-LIVER_ONT.P2_ALU.CAPTURE", "@id": "/libraries/70625351-b4f9-4bee-87d7-15f1306032e5/", "uuid": "70625351-b4f9-4bee-87d7-15f1306032e5", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "enzymes": ["Cas9"], "description": "Library preparation for TenCATS capture of L1H and Alu elements", "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "strand": "Unstranded", "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "amplification_method": ["Not Applicable"], "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSRKI36FO", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST001-LIVER_ONT.P2_ALU.CAPTURE", "uuid": "1d42b253-1bf7-4621-9c11-8568b950d433", "tags": ["ready_to_release"], "sequencing": {"read_type": "Single-end", "target_coverage": 63.0, "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST001-LIVER_ONT.P2_ALU.CAPTURE", "on_target_rate": 0.242, "uuid": "fa6d5d07-6291-409f-9d13-80b1e770d7f1", "submitted_id": "UMICH_SEQUENCING_ST001-LIVER_ONT.P2_ALU.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 4300, "@id": "/Sequencing/fa6d5d07-6291-409f-9d13-80b1e770d7f1/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "upload_key": "533e7a02-a0f1-40de-b054-bc6f1c7c5912/SMAARWX5Z3UE.bam", "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:48.164763+00:00", "uploaded": "2025-11-06T02:35:37.745697+00:00", "uploading": "2025-10-06T20:39:05.374066+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:48.164763+00:00", "public_release": "2026-01-30T17:26:48.164763+00:00"}}, "display_title": "ST001-1A-XX-M22-E028-umich-SMAARWX5Z3UE-minimap2_2.26_GRCh38.aligned.sorted.bam", "accession": "SMAARWX5Z3UE", "@id": "/aligned-reads/533e7a02-a0f1-40de-b054-bc6f1c7c5912/", "uuid": "533e7a02-a0f1-40de-b054-bc6f1c7c5912", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST001-1A_LIVER", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-4300-R10.4.1"}, "@id": "/file-sets/1d42b253-1bf7-4621-9c11-8568b950d433/", "last_modified": {"date_modified": "2026-01-30T17:26:48.768370+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}, {"tissue_types": ["Liver"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "date_created": "2025-10-06T20:39:03.558924+00:00", "@type": ["FileSet", "Item"], "display_title": "UMICH_FILE-SET_ST001-LIVER_ONT.P2_L1H.CAPTURE", "libraries": [{"dna_target": ["L1H"], "analytes": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Analyte", "Item"], "display_title": "UMICH_ANALYTE_ST001-1A-101X_LIVER", "@id": "/analytes/f0cad2a2-e42b-4860-ae77-2593ca79e17f/", "accession": "SMAAN15PANIC", "uuid": "f0cad2a2-e42b-4860-ae77-2593ca79e17f", "samples": [{"sample_sources": [{"code": "ST001-1A", "donor": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Donor", "AbstractDonor", "Item"], "display_title": "ST001", "accession": "SMADOWNO1XMS", "@id": "/donors/3039a6ca-9849-432d-ad49-2c5630bcbee7/", "uuid": "3039a6ca-9849-432d-ad49-2c5630bcbee7", "status": "open"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "uberon_id": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["OntologyTerm", "Item"], "display_title": "right lobe of liver", "@id": "/ontology-terms/a68d2524-e527-43b6-bf7d-4e4fd7a9ce8b/", "uuid": "a68d2524-e527-43b6-bf7d-4e4fd7a9ce8b", "status": "open"}, "@type": ["Tissue", "SampleSource", "Item"], "display_title": "ST001-1A", "@id": "/tissues/f84d3b01-bef0-46b3-b87a-6542b797730d/", "uuid": "f84d3b01-bef0-46b3-b87a-6542b797730d", "submitted_id": "NDRI_TISSUE_ST001-1A_LIVER", "status": "open"}], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["TissueSample", "Sample", "Item"], "display_title": "ST001-1A-101X", "@id": "/tissue-samples/2acd0a3d-3bb1-4f45-9f03-2123b498c3bc/", "accession": "SMATSGWX1T9D", "uuid": "2acd0a3d-3bb1-4f45-9f03-2123b498c3bc", "status": "open"}], "status": "open"}], "preparation_date": "2025-08-06", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "guide_sequence": ["CTAATGTGTCATCTAGCATT"], "assay": {"identifier": "tencats", "code": "028", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Assay", "Item"], "display_title": "TEnCATS", "@id": "/assays/53e58de8-d175-4788-8f69-00ec505b1a42/", "uuid": "53e58de8-d175-4788-8f69-00ec505b1a42", "status": "open"}, "@type": ["Library", "Item"], "display_title": "UMICH_LIBRARY_ST001-LIVER_ONT.P2_L1H.CAPTURE", "@id": "/libraries/3310b55c-69ec-4de1-b809-d302408b81e9/", "uuid": "3310b55c-69ec-4de1-b809-d302408b81e9", "status": "open", "library_preparation": {"size_selection_method": ["Magnetic Beads"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "adapter_inclusion_method": ["Ligation"], "@type": ["LibraryPreparation", "Preparation", "Item"], "display_title": "UMICH_LIBRARY-PREPARATION_TENCATS_ONT_LSK114.CAPTURE", "description": "Library preparation for TenCATS capture of L1H and Alu elements", "enzymes": ["Cas9"], "uuid": "7246549e-0df0-4729-ae7a-c99e4733f5da", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "vendor": "Oxford Nanopore Technologies", "@type": ["PreparationKit", "Item"], "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "version": "14.0", "status": "open"}], "strand": "Unstranded", "amplification_method": ["Not Applicable"], "@id": "/library-preparations/7246549e-0df0-4729-ae7a-c99e4733f5da/", "fragmentation_method": ["Not Applicable"], "status": "open"}}], "description": "PromethION", "submitted_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.0d565156-00db-4948-82fe-021d151a5daf", "userid.e34b090e-aa4e-494c-9bb3-79d0dbce0301"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "William Feng", "@id": "/users/0d565156-00db-4948-82fe-021d151a5daf/", "uuid": "0d565156-00db-4948-82fe-021d151a5daf", "status": "current"}, "accession": "SMAFSA2FJR81", "consortia": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Consortium", "Item"], "display_title": "SMaHT", "@id": "/consortia/358aed10-9b9d-4e26-ab84-4bd162da182b/", "uuid": "358aed10-9b9d-4e26-ab84-4bd162da182b", "status": "open"}], "submitted_id": "UMICH_FILE-SET_ST001-LIVER_ONT.P2_L1H.CAPTURE", "uuid": "173cfe11-cd00-40b2-b82e-ffd1821f106b", "tags": ["ready_to_release"], "sequencing": {"target_coverage": 498.0, "read_type": "Single-end", "flow_cell": "R10.4.1", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencing", "Item"], "display_title": "UMICH_SEQUENCING_ST001-LIVER_ONT.P2_L1H.CAPTURE", "on_target_rate": 0.1649, "uuid": "65c496b6-38c3-45b7-9e1b-e7e5c40a739b", "submitted_id": "UMICH_SEQUENCING_ST001-LIVER_ONT.P2_L1H.CAPTURE", "preparation_kits": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "catalog_number": "SQK-LSK114", "@type": ["PreparationKit", "Item"], "vendor": "Oxford Nanopore Technologies", "display_title": "Ligation Sequencing Kit V14", "@id": "/preparation-kits/df9ee03a-dda6-4864-aa29-27934d728824/", "title": "Ligation Sequencing Kit V14", "version": "14.0", "uuid": "df9ee03a-dda6-4864-aa29-27934d728824", "status": "open"}], "sequencer": {"identifier": "ont_promethion_2_solo", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["Sequencer", "Item"], "display_title": "ONT PromethION 2 Solo", "@id": "/sequencers/849aed8f-95a5-4be6-a71e-87a05aaacf20/", "uuid": "849aed8f-95a5-4be6-a71e-87a05aaacf20", "status": "open"}, "target_read_length": 3100, "@id": "/Sequencing/65c496b6-38c3-45b7-9e1b-e7e5c40a739b/", "status": "open"}, "schema_version": "2", "submission_centers": [{"identifier": "umich_ttd", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["SubmissionCenter", "Item"], "display_title": "UMICH TTD", "@id": "/submission-centers/66352171-aba7-4847-8f94-a017700dc627/", "uuid": "66352171-aba7-4847-8f94-a017700dc627", "status": "open"}], "files": [{"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "upload_key": "72ad3fa6-33c5-4e1e-b0a5-d6442ac6db24/SMAARE1MTVYO.bam", "@type": ["AlignedReads", "SubmittedFile", "File", "Item"], "file_status_tracking": {"status_tracking": {"protected": "2026-01-30T17:26:51.360155+00:00", "uploaded": "2025-11-06T02:38:07.215696+00:00", "uploading": "2025-10-06T20:39:07.424878+00:00", "protected_date": "2026-01-30"}, "release_dates": {"initial_release_date": "2026-01-30", "public_release_date": "2026-01-30", "initial_release": "2026-01-30T17:26:51.360155+00:00", "public_release": "2026-01-30T17:26:51.360155+00:00"}}, "display_title": "ST001-1A-XX-M22-E028-umich-SMAARE1MTVYO-minimap2_2.26_GRCh38.aligned.sorted.bam", "accession": "SMAARE1MTVYO", "@id": "/aligned-reads/72ad3fa6-33c5-4e1e-b0a5-d6442ac6db24/", "uuid": "72ad3fa6-33c5-4e1e-b0a5-d6442ac6db24", "file_format": {"principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "@type": ["FileFormat", "Item"], "display_title": "bam", "@id": "/file-formats/d13d06cf-218e-4f61-aaf0-91f226248b3c/", "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "status": "open"}, "status": "protected"}], "file_group": {"sample_source": "NDRI_TISSUE_ST001-1A_LIVER", "submission_center": "umich_ttd", "assay": "tencats", "group_tag": "", "sequencing": "ont_promethion_2_solo-Single-end-3100-R10.4.1"}, "@id": "/file-sets/173cfe11-cd00-40b2-b82e-ffd1821f106b/", "last_modified": {"date_modified": "2026-01-30T17:26:52.110983+00:00", "modified_by": {"principals_allowed": {"view": ["group.admin", "remoteuser.EMBED", "remoteuser.INDEXER", "role.owner", "userid.45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "userid.f9524d43-01b5-4b71-94c6-32d2d09c2222"], "edit": ["group.admin"]}, "@type": ["User", "Item"], "display_title": "Alexander Veit", "@id": "/users/45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15/", "uuid": "45ac3b0a-6640-4ccc-8ba7-e4cc7c778c15", "status": "current"}}, "status": "open"}], "notification": "Success", "sort": {"date_created": {"order": "desc", "unmapped_type": "keyword"}, "label": {"order": "asc", "missing": "_last", "unmapped_type": "keyword"}}, "clear_filters": "/search/?type=FileSet", "total": 581, "aggregations": {}, "actions": null, "columns": {"display_title": {"title": "Title", "order": -1000}, "submission_centers.display_title": {"title": "Submitted By"}, "libraries.assay.display_title": {"title": "Assay"}, "sequencing.sequencer.display_title": {"title": "Sequencer"}, "status": {"title": "Status", "default_hidden": true, "order": 980}, "date_created": {"title": "Date Created", "colTitle": "Created", "default_hidden": true, "order": 1000}}}