IGVFDS1476FCGD

1{
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4    "@type": [
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9    "accession": "IGVFDS1476FCGD",
10    "aliases": [
11        "igvf:corces_measurementSet_X009_G1_RNA"
12    ],
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15        "assay_slims": [
16            "gene expression"
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18        "status": "released",
19        "term_name": "single-nucleus RNA sequencing assay"
20    },
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359            {
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361                "detail": "Preview human donor [IGVFDO8451NMBP](/human-donors/IGVFDO8451NMBP/) has in progress subobject phenotypic feature [49ab6d82-1b46-419b-8cc4-45d027be56fe](/phenotypic-features/49ab6d82-1b46-419b-8cc4-45d027be56fe/).",
362                "level": 30,
363                "level_name": "INTERNAL_ACTION",
364                "name": "audit_item_status",
365                "path": "/human-donors/IGVFDO8451NMBP/"
366            },
367            {
368                "category": "mismatched status",
369                "detail": "Preview human donor [IGVFDO8451NMBP](/human-donors/IGVFDO8451NMBP/) has in progress subobject phenotypic feature [11fbe4b3-7cc6-46a9-a210-6deab3bc4d79](/phenotypic-features/11fbe4b3-7cc6-46a9-a210-6deab3bc4d79/).",
370                "level": 30,
371                "level_name": "INTERNAL_ACTION",
372                "name": "audit_item_status",
373                "path": "/human-donors/IGVFDO8451NMBP/"
374            },
375            {
376                "category": "mismatched status",
377                "detail": "Preview human donor [IGVFDO3971UIZC](/human-donors/IGVFDO3971UIZC/) has in progress subobject phenotypic feature [f57d3e32-48bd-4719-8d01-68046dd4734c](/phenotypic-features/f57d3e32-48bd-4719-8d01-68046dd4734c/).",
378                "level": 30,
379                "level_name": "INTERNAL_ACTION",
380                "name": "audit_item_status",
381                "path": "/human-donors/IGVFDO3971UIZC/"
382            },
383            {
384                "category": "mismatched status",
385                "detail": "Preview human donor [IGVFDO3971UIZC](/human-donors/IGVFDO3971UIZC/) has in progress subobject phenotypic feature [e4feb5fc-ff23-4699-a4d2-620d59dcdd3e](/phenotypic-features/e4feb5fc-ff23-4699-a4d2-620d59dcdd3e/).",
386                "level": 30,
387                "level_name": "INTERNAL_ACTION",
388                "name": "audit_item_status",
389                "path": "/human-donors/IGVFDO3971UIZC/"
390            },
391            {
392                "category": "mismatched status",
393                "detail": "Preview human donor [IGVFDO3971UIZC](/human-donors/IGVFDO3971UIZC/) has in progress subobject phenotypic feature [22131022-5110-4ae2-91a6-98c3dcc35ee0](/phenotypic-features/22131022-5110-4ae2-91a6-98c3dcc35ee0/).",
394                "level": 30,
395                "level_name": "INTERNAL_ACTION",
396                "name": "audit_item_status",
397                "path": "/human-donors/IGVFDO3971UIZC/"
398            },
399            {
400                "category": "mismatched status",
401                "detail": "Preview human donor [IGVFDO3971UIZC](/human-donors/IGVFDO3971UIZC/) has in progress subobject phenotypic feature [30a806f6-8eeb-410a-a2db-f5b64f11b294](/phenotypic-features/30a806f6-8eeb-410a-a2db-f5b64f11b294/).",
402                "level": 30,
403                "level_name": "INTERNAL_ACTION",
404                "name": "audit_item_status",
405                "path": "/human-donors/IGVFDO3971UIZC/"
406            },
407            {
408                "category": "mismatched status",
409                "detail": "Preview human donor [IGVFDO3971UIZC](/human-donors/IGVFDO3971UIZC/) has in progress subobject phenotypic feature [8e88e2ab-61fc-482b-a4b5-416755a847bc](/phenotypic-features/8e88e2ab-61fc-482b-a4b5-416755a847bc/).",
410                "level": 30,
411                "level_name": "INTERNAL_ACTION",
412                "name": "audit_item_status",
413                "path": "/human-donors/IGVFDO3971UIZC/"
414            },
415            {
416                "category": "mismatched status",
417                "detail": "Preview human donor [IGVFDO8891KXRJ](/human-donors/IGVFDO8891KXRJ/) has in progress subobject phenotypic feature [f2101a81-e55f-43bb-a630-eb88c8dc202b](/phenotypic-features/f2101a81-e55f-43bb-a630-eb88c8dc202b/).",
418                "level": 30,
419                "level_name": "INTERNAL_ACTION",
420                "name": "audit_item_status",
421                "path": "/human-donors/IGVFDO8891KXRJ/"
422            },
423            {
424                "category": "mismatched status",
425                "detail": "Preview human donor [IGVFDO8891KXRJ](/human-donors/IGVFDO8891KXRJ/) has in progress subobject phenotypic feature [6490cb03-ac22-485a-aa91-ac5cc4ac399c](/phenotypic-features/6490cb03-ac22-485a-aa91-ac5cc4ac399c/).",
426                "level": 30,
427                "level_name": "INTERNAL_ACTION",
428                "name": "audit_item_status",
429                "path": "/human-donors/IGVFDO8891KXRJ/"
430            },
431            {
432                "category": "mismatched status",
433                "detail": "Preview human donor [IGVFDO8891KXRJ](/human-donors/IGVFDO8891KXRJ/) has in progress subobject phenotypic feature [ba7722d9-75b0-4b99-ab90-566c5038d6dc](/phenotypic-features/ba7722d9-75b0-4b99-ab90-566c5038d6dc/).",
434                "level": 30,
435                "level_name": "INTERNAL_ACTION",
436                "name": "audit_item_status",
437                "path": "/human-donors/IGVFDO8891KXRJ/"
438            },
439            {
440                "category": "mismatched status",
441                "detail": "Preview human donor [IGVFDO8891KXRJ](/human-donors/IGVFDO8891KXRJ/) has in progress subobject phenotypic feature [67d610ff-1188-474e-b062-65d1c3cd425e](/phenotypic-features/67d610ff-1188-474e-b062-65d1c3cd425e/).",
442                "level": 30,
443                "level_name": "INTERNAL_ACTION",
444                "name": "audit_item_status",
445                "path": "/human-donors/IGVFDO8891KXRJ/"
446            },
447            {
448                "category": "mismatched status",
449                "detail": "Preview human donor [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [52f2a871-4f9a-4125-8b75-21b86db71234](/phenotypic-features/52f2a871-4f9a-4125-8b75-21b86db71234/).",
450                "level": 30,
451                "level_name": "INTERNAL_ACTION",
452                "name": "audit_item_status",
453                "path": "/human-donors/IGVFDO7306YMGC/"
454            },
455            {
456                "category": "mismatched status",
457                "detail": "Preview human donor [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [6f2ca47b-41f5-4df7-873b-985b82301aca](/phenotypic-features/6f2ca47b-41f5-4df7-873b-985b82301aca/).",
458                "level": 30,
459                "level_name": "INTERNAL_ACTION",
460                "name": "audit_item_status",
461                "path": "/human-donors/IGVFDO7306YMGC/"
462            },
463            {
464                "category": "mismatched status",
465                "detail": "Preview human donor [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [c2d841ed-9a79-4029-8f19-938166bb96ee](/phenotypic-features/c2d841ed-9a79-4029-8f19-938166bb96ee/).",
466                "level": 30,
467                "level_name": "INTERNAL_ACTION",
468                "name": "audit_item_status",
469                "path": "/human-donors/IGVFDO7306YMGC/"
470            },
471            {
472                "category": "mismatched status",
473                "detail": "Preview human donor [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [b7d1671f-0cb9-42ce-84bf-70d7508a2dc8](/phenotypic-features/b7d1671f-0cb9-42ce-84bf-70d7508a2dc8/).",
474                "level": 30,
475                "level_name": "INTERNAL_ACTION",
476                "name": "audit_item_status",
477                "path": "/human-donors/IGVFDO7306YMGC/"
478            },
479            {
480                "category": "mismatched status",
481                "detail": "Preview human donor [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [cc8814f1-9ac1-45dc-ac47-102a624b5880](/phenotypic-features/cc8814f1-9ac1-45dc-ac47-102a624b5880/).",
482                "level": 30,
483                "level_name": "INTERNAL_ACTION",
484                "name": "audit_item_status",
485                "path": "/human-donors/IGVFDO7306YMGC/"
486            },
487            {
488                "category": "mismatched status",
489                "detail": "Preview human donor [IGVFDO1464XWYC](/human-donors/IGVFDO1464XWYC/) has in progress subobject phenotypic feature [5966062a-b342-4b70-9aa9-9db9c46d5bb3](/phenotypic-features/5966062a-b342-4b70-9aa9-9db9c46d5bb3/).",
490                "level": 30,
491                "level_name": "INTERNAL_ACTION",
492                "name": "audit_item_status",
493                "path": "/human-donors/IGVFDO1464XWYC/"
494            },
495            {
496                "category": "mismatched status",
497                "detail": "Preview human donor [IGVFDO1464XWYC](/human-donors/IGVFDO1464XWYC/) has in progress subobject phenotypic feature [b7673a14-200c-4d11-99af-42748f5f2b5a](/phenotypic-features/b7673a14-200c-4d11-99af-42748f5f2b5a/).",
498                "level": 30,
499                "level_name": "INTERNAL_ACTION",
500                "name": "audit_item_status",
501                "path": "/human-donors/IGVFDO1464XWYC/"
502            },
503            {
504                "category": "mismatched status",
505                "detail": "Preview human donor [IGVFDO1464XWYC](/human-donors/IGVFDO1464XWYC/) has in progress subobject phenotypic feature [0944c07c-192b-4750-9fa2-98e9d416951d](/phenotypic-features/0944c07c-192b-4750-9fa2-98e9d416951d/).",
506                "level": 30,
507                "level_name": "INTERNAL_ACTION",
508                "name": "audit_item_status",
509                "path": "/human-donors/IGVFDO1464XWYC/"
510            },
511            {
512                "category": "mismatched status",
513                "detail": "Preview human donor [IGVFDO1464XWYC](/human-donors/IGVFDO1464XWYC/) has in progress subobject phenotypic feature [150696e6-cb05-4577-bfa3-59c11882d502](/phenotypic-features/150696e6-cb05-4577-bfa3-59c11882d502/).",
514                "level": 30,
515                "level_name": "INTERNAL_ACTION",
516                "name": "audit_item_status",
517                "path": "/human-donors/IGVFDO1464XWYC/"
518            },
519            {
520                "category": "mismatched status",
521                "detail": "Preview human donor [IGVFDO1464XWYC](/human-donors/IGVFDO1464XWYC/) has in progress subobject phenotypic feature [2853f35c-e0bb-40d8-8f0a-6d998a7db51a](/phenotypic-features/2853f35c-e0bb-40d8-8f0a-6d998a7db51a/).",
522                "level": 30,
523                "level_name": "INTERNAL_ACTION",
524                "name": "audit_item_status",
525                "path": "/human-donors/IGVFDO1464XWYC/"
526            }
527        ],
528        "NOT_COMPLIANT": [
529            {
530                "category": "missing sequence specification",
531                "detail": "Measurement set [IGVFDS1476FCGD](/measurement-sets/IGVFDS1476FCGD/) has sequence file(s): [IGVFFI7388LCIJ](/sequence-files/IGVFFI7388LCIJ/), [IGVFFI9444MAEC](/sequence-files/IGVFFI9444MAEC/), [IGVFFI8191CHCB](/sequence-files/IGVFFI8191CHCB/), [IGVFFI9308WNTD](/sequence-files/IGVFFI9308WNTD/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
532                "level": 50,
533                "level_name": "NOT_COMPLIANT",
534                "name": "audit_missing_seqspec",
535                "path": "/measurement-sets/IGVFDS1476FCGD/"
536            },
537            {
538                "category": "missing strand specificity",
539                "detail": "Measurement set [IGVFDS1476FCGD](/measurement-sets/IGVFDS1476FCGD/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
540                "level": 50,
541                "level_name": "NOT_COMPLIANT",
542                "name": "audit_missing_strand_specificity",
543                "path": "/measurement-sets/IGVFDS1476FCGD/"
544            }
545        ],
546        "WARNING": [
547            {
548                "category": "missing analysis",
549                "detail": "Measurement set [IGVFDS1476FCGD](/measurement-sets/IGVFDS1476FCGD/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
550                "level": 40,
551                "level_name": "WARNING",
552                "name": "audit_input_for",
553                "path": "/measurement-sets/IGVFDS1476FCGD/"
554            }
555        ]
556    },
557    "award": {
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560        "contact_pi": {
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562            "title": "Ansuman Satpathy"
563        },
564        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
565    },
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567    "controlled_access": false,
568    "creation_timestamp": "2025-03-19T20:00:18.469361+00:00",
569    "data_use_limitation_summaries": [
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571    ],
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578            ],
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582        },
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588            ],
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592        },
593        {
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623        {
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653        {
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792    "onlist_files": [
793        "/tabular-files/IGVFFI8751YQRY/"
794    ],
795    "onlist_method": "no combination",
796    "preferred_assay_title": "10x multiome",
797    "protocols": [
798        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
799    ],
800    "related_multiome_datasets": [
801        {
802            "@id": "/measurement-sets/IGVFDS2827YRAB/",
803            "accession": "IGVFDS2827YRAB",
804            "status": "preview"
805        }
806    ],
807    "samples": [
808        {
809            "@id": "/multiplexed-samples/IGVFSM9375ZKWX/",
810            "@type": [
811                "MultiplexedSample",
812                "Sample",
813                "Item"
814            ],
815            "accession": "IGVFSM9375ZKWX",
816            "aliases": [
817                "igvf:corces_multiplexedSample_X009_G1"
818            ],
819            "classifications": [
820                "tissue",
821                "multiplexed sample"
822            ],
823            "disease_terms": [
824                {
825                    "@id": "/phenotype-terms/DOID_0080832/",
826                    "status": "in progress",
827                    "term_name": "mild cognitive impairment"
828                },
829                {
830                    "@id": "/phenotype-terms/DOID_14330/",
831                    "status": "in progress",
832                    "term_name": "Parkinson's disease"
833                },
834                {
835                    "@id": "/phenotype-terms/DOID_9246/",
836                    "status": "in progress",
837                    "term_name": "cerebral amyloid angiopathy"
838                }
839            ],
840            "institutional_certificates": [
841                {
842                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
843                    "certificate_identifier": "IP115-05",
844                    "controlled_access": false,
845                    "status": "in progress"
846                }
847            ],
848            "modifications": [],
849            "sample_terms": [
850                {
851                    "@id": "/sample-terms/UBERON_0001874/",
852                    "@type": [
853                        "SampleTerm",
854                        "OntologyTerm",
855                        "Item"
856                    ],
857                    "status": "preview",
858                    "summary": "putamen",
859                    "term_name": "putamen"
860                },
861                {
862                    "@id": "/sample-terms/UBERON_0002038/",
863                    "@type": [
864                        "SampleTerm",
865                        "OntologyTerm",
866                        "Item"
867                    ],
868                    "status": "preview",
869                    "summary": "substantia nigra",
870                    "term_name": "substantia nigra"
871                },
872                {
873                    "@id": "/sample-terms/UBERON_0002129/",
874                    "@type": [
875                        "SampleTerm",
876                        "OntologyTerm",
877                        "Item"
878                    ],
879                    "status": "preview",
880                    "summary": "cerebellar cortex",
881                    "term_name": "cerebellar cortex"
882                },
883                {
884                    "@id": "/sample-terms/UBERON_0002740/",
885                    "@type": [
886                        "SampleTerm",
887                        "OntologyTerm",
888                        "Item"
889                    ],
890                    "status": "preview",
891                    "summary": "posterior cingulate gyrus",
892                    "term_name": "posterior cingulate gyrus"
893                },
894                {
895                    "@id": "/sample-terms/UBERON_0002771/",
896                    "@type": [
897                        "SampleTerm",
898                        "OntologyTerm",
899                        "Item"
900                    ],
901                    "status": "preview",
902                    "summary": "middle temporal gyrus",
903                    "term_name": "middle temporal gyrus"
904                }
905            ],
906            "status": "preview",
907            "summary": "multiplexed sample: Homo sapiens (male, 83 years) posterior cingulate gyrus tissue associated with Parkinson's disease; Homo sapiens (male, 78 years) cerebellar cortex tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; ... and 10 more samples",
908            "taxa": "Homo sapiens",
909            "treatments": []
910        }
911    ],
912    "schema_version": "26",
913    "status": "preview",
914    "submitted_by": {
915        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
916        "title": "Ryan Corces"
917    },
918    "submitted_files_timestamp": "2025-03-20T00:47:45.693168+00:00",
919    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
920    "uuid": "c25956ab-dc0e-459d-a771-8033bb62e38d"
921}