IGVFDS3718PAFU

1{
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10    "aliases": [
11        "igvf:corces_measurementSet_X014_G7_RNA"
12    ],
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14        "@id": "/assay-terms/OBI_0003109/",
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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362                "level": 30,
363                "level_name": "INTERNAL_ACTION",
364                "name": "audit_item_status",
365                "path": "/human-donors/IGVFDO3795BUZW/"
366            },
367            {
368                "category": "mismatched status",
369                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [0cd59ebe-1db1-4f78-94b0-874fcf8fe239](/phenotypic-features/0cd59ebe-1db1-4f78-94b0-874fcf8fe239/).",
370                "level": 30,
371                "level_name": "INTERNAL_ACTION",
372                "name": "audit_item_status",
373                "path": "/human-donors/IGVFDO1469WVVS/"
374            },
375            {
376                "category": "mismatched status",
377                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [fd6110d1-a29e-4225-a5e6-27a7614bcdd7](/phenotypic-features/fd6110d1-a29e-4225-a5e6-27a7614bcdd7/).",
378                "level": 30,
379                "level_name": "INTERNAL_ACTION",
380                "name": "audit_item_status",
381                "path": "/human-donors/IGVFDO1469WVVS/"
382            },
383            {
384                "category": "mismatched status",
385                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [66e32efb-7f85-4402-a04c-fece8128ee8e](/phenotypic-features/66e32efb-7f85-4402-a04c-fece8128ee8e/).",
386                "level": 30,
387                "level_name": "INTERNAL_ACTION",
388                "name": "audit_item_status",
389                "path": "/human-donors/IGVFDO1469WVVS/"
390            },
391            {
392                "category": "mismatched status",
393                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [5ec82856-d387-4727-9473-c60628ddce27](/phenotypic-features/5ec82856-d387-4727-9473-c60628ddce27/).",
394                "level": 30,
395                "level_name": "INTERNAL_ACTION",
396                "name": "audit_item_status",
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398            },
399            {
400                "category": "mismatched status",
401                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [a945aea6-1bca-4a51-a030-e44b27e81d2a](/phenotypic-features/a945aea6-1bca-4a51-a030-e44b27e81d2a/).",
402                "level": 30,
403                "level_name": "INTERNAL_ACTION",
404                "name": "audit_item_status",
405                "path": "/human-donors/IGVFDO1469WVVS/"
406            },
407            {
408                "category": "mismatched status",
409                "detail": "Preview human donor [IGVFDO1469WVVS](/human-donors/IGVFDO1469WVVS/) has in progress subobject phenotypic feature [42c6269c-25ee-4326-b51c-086f9665bf75](/phenotypic-features/42c6269c-25ee-4326-b51c-086f9665bf75/).",
410                "level": 30,
411                "level_name": "INTERNAL_ACTION",
412                "name": "audit_item_status",
413                "path": "/human-donors/IGVFDO1469WVVS/"
414            },
415            {
416                "category": "mismatched status",
417                "detail": "Preview human donor [IGVFDO3497MBPK](/human-donors/IGVFDO3497MBPK/) has in progress subobject phenotypic feature [db57ba6b-00fe-4b3c-ade7-bd716278659e](/phenotypic-features/db57ba6b-00fe-4b3c-ade7-bd716278659e/).",
418                "level": 30,
419                "level_name": "INTERNAL_ACTION",
420                "name": "audit_item_status",
421                "path": "/human-donors/IGVFDO3497MBPK/"
422            },
423            {
424                "category": "mismatched status",
425                "detail": "Preview human donor [IGVFDO3497MBPK](/human-donors/IGVFDO3497MBPK/) has in progress subobject phenotypic feature [53fadfcd-d570-414f-aed0-a4e638d92474](/phenotypic-features/53fadfcd-d570-414f-aed0-a4e638d92474/).",
426                "level": 30,
427                "level_name": "INTERNAL_ACTION",
428                "name": "audit_item_status",
429                "path": "/human-donors/IGVFDO3497MBPK/"
430            },
431            {
432                "category": "mismatched status",
433                "detail": "Preview human donor [IGVFDO3497MBPK](/human-donors/IGVFDO3497MBPK/) has in progress subobject phenotypic feature [559f0c1c-c480-4fa6-858c-d192247d30ba](/phenotypic-features/559f0c1c-c480-4fa6-858c-d192247d30ba/).",
434                "level": 30,
435                "level_name": "INTERNAL_ACTION",
436                "name": "audit_item_status",
437                "path": "/human-donors/IGVFDO3497MBPK/"
438            },
439            {
440                "category": "mismatched status",
441                "detail": "Preview human donor [IGVFDO3497MBPK](/human-donors/IGVFDO3497MBPK/) has in progress subobject phenotypic feature [137c4c1b-d3a8-407e-aaaf-ccfc2822d20d](/phenotypic-features/137c4c1b-d3a8-407e-aaaf-ccfc2822d20d/).",
442                "level": 30,
443                "level_name": "INTERNAL_ACTION",
444                "name": "audit_item_status",
445                "path": "/human-donors/IGVFDO3497MBPK/"
446            },
447            {
448                "category": "mismatched status",
449                "detail": "Preview human donor [IGVFDO3497MBPK](/human-donors/IGVFDO3497MBPK/) has in progress subobject phenotypic feature [80146ba9-5b2d-46e0-908e-ac8e7186fa69](/phenotypic-features/80146ba9-5b2d-46e0-908e-ac8e7186fa69/).",
450                "level": 30,
451                "level_name": "INTERNAL_ACTION",
452                "name": "audit_item_status",
453                "path": "/human-donors/IGVFDO3497MBPK/"
454            },
455            {
456                "category": "mismatched status",
457                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [d900f184-9bf7-4b9c-8d20-0d40c6b16435](/phenotypic-features/d900f184-9bf7-4b9c-8d20-0d40c6b16435/).",
458                "level": 30,
459                "level_name": "INTERNAL_ACTION",
460                "name": "audit_item_status",
461                "path": "/human-donors/IGVFDO8344LUQZ/"
462            },
463            {
464                "category": "mismatched status",
465                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [cd2525eb-a90d-47c1-a053-cd3376cd23d1](/phenotypic-features/cd2525eb-a90d-47c1-a053-cd3376cd23d1/).",
466                "level": 30,
467                "level_name": "INTERNAL_ACTION",
468                "name": "audit_item_status",
469                "path": "/human-donors/IGVFDO8344LUQZ/"
470            },
471            {
472                "category": "mismatched status",
473                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [1961d5fc-9987-47f0-8cdf-9dae2203185c](/phenotypic-features/1961d5fc-9987-47f0-8cdf-9dae2203185c/).",
474                "level": 30,
475                "level_name": "INTERNAL_ACTION",
476                "name": "audit_item_status",
477                "path": "/human-donors/IGVFDO8344LUQZ/"
478            },
479            {
480                "category": "mismatched status",
481                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [ef944fd3-8635-4e0f-bad8-48136e7c6408](/phenotypic-features/ef944fd3-8635-4e0f-bad8-48136e7c6408/).",
482                "level": 30,
483                "level_name": "INTERNAL_ACTION",
484                "name": "audit_item_status",
485                "path": "/human-donors/IGVFDO8344LUQZ/"
486            },
487            {
488                "category": "mismatched status",
489                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [93e7b543-5ab9-4cb4-8a10-9d9a7b950b6b](/phenotypic-features/93e7b543-5ab9-4cb4-8a10-9d9a7b950b6b/).",
490                "level": 30,
491                "level_name": "INTERNAL_ACTION",
492                "name": "audit_item_status",
493                "path": "/human-donors/IGVFDO8344LUQZ/"
494            },
495            {
496                "category": "mismatched status",
497                "detail": "Preview human donor [IGVFDO8344LUQZ](/human-donors/IGVFDO8344LUQZ/) has in progress subobject phenotypic feature [025a53bb-7c23-42cb-9752-3516f17f6187](/phenotypic-features/025a53bb-7c23-42cb-9752-3516f17f6187/).",
498                "level": 30,
499                "level_name": "INTERNAL_ACTION",
500                "name": "audit_item_status",
501                "path": "/human-donors/IGVFDO8344LUQZ/"
502            },
503            {
504                "category": "mismatched status",
505                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [574c872c-cbb9-4ac3-8588-96c92bfb2178](/phenotypic-features/574c872c-cbb9-4ac3-8588-96c92bfb2178/).",
506                "level": 30,
507                "level_name": "INTERNAL_ACTION",
508                "name": "audit_item_status",
509                "path": "/human-donors/IGVFDO1627RQLG/"
510            },
511            {
512                "category": "mismatched status",
513                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [3fa71c98-89df-4ad6-89e6-2b9f628661b6](/phenotypic-features/3fa71c98-89df-4ad6-89e6-2b9f628661b6/).",
514                "level": 30,
515                "level_name": "INTERNAL_ACTION",
516                "name": "audit_item_status",
517                "path": "/human-donors/IGVFDO1627RQLG/"
518            },
519            {
520                "category": "mismatched status",
521                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [6fd55d81-8294-4fbb-bfa3-5cd753903b06](/phenotypic-features/6fd55d81-8294-4fbb-bfa3-5cd753903b06/).",
522                "level": 30,
523                "level_name": "INTERNAL_ACTION",
524                "name": "audit_item_status",
525                "path": "/human-donors/IGVFDO1627RQLG/"
526            },
527            {
528                "category": "mismatched status",
529                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [29b01022-547a-453c-9e54-43b15bdbfd90](/phenotypic-features/29b01022-547a-453c-9e54-43b15bdbfd90/).",
530                "level": 30,
531                "level_name": "INTERNAL_ACTION",
532                "name": "audit_item_status",
533                "path": "/human-donors/IGVFDO1627RQLG/"
534            },
535            {
536                "category": "mismatched status",
537                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [a7aae585-7ced-40aa-861f-6c2d4350a8c0](/phenotypic-features/a7aae585-7ced-40aa-861f-6c2d4350a8c0/).",
538                "level": 30,
539                "level_name": "INTERNAL_ACTION",
540                "name": "audit_item_status",
541                "path": "/human-donors/IGVFDO1627RQLG/"
542            },
543            {
544                "category": "mismatched status",
545                "detail": "Preview human donor [IGVFDO1627RQLG](/human-donors/IGVFDO1627RQLG/) has in progress subobject phenotypic feature [01ea38fe-9967-4087-b0d5-04259cc56561](/phenotypic-features/01ea38fe-9967-4087-b0d5-04259cc56561/).",
546                "level": 30,
547                "level_name": "INTERNAL_ACTION",
548                "name": "audit_item_status",
549                "path": "/human-donors/IGVFDO1627RQLG/"
550            }
551        ],
552        "NOT_COMPLIANT": [
553            {
554                "category": "missing sequence specification",
555                "detail": "Measurement set [IGVFDS3718PAFU](/measurement-sets/IGVFDS3718PAFU/) has sequence file(s): [IGVFFI2642EVUB](/sequence-files/IGVFFI2642EVUB/), [IGVFFI3992YZBJ](/sequence-files/IGVFFI3992YZBJ/), [IGVFFI7107JHPK](/sequence-files/IGVFFI7107JHPK/), [IGVFFI3141LMMO](/sequence-files/IGVFFI3141LMMO/) 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.",
556                "level": 50,
557                "level_name": "NOT_COMPLIANT",
558                "name": "audit_missing_seqspec",
559                "path": "/measurement-sets/IGVFDS3718PAFU/"
560            },
561            {
562                "category": "missing strand specificity",
563                "detail": "Measurement set [IGVFDS3718PAFU](/measurement-sets/IGVFDS3718PAFU/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
564                "level": 50,
565                "level_name": "NOT_COMPLIANT",
566                "name": "audit_missing_strand_specificity",
567                "path": "/measurement-sets/IGVFDS3718PAFU/"
568            }
569        ],
570        "WARNING": [
571            {
572                "category": "missing analysis",
573                "detail": "Measurement set [IGVFDS3718PAFU](/measurement-sets/IGVFDS3718PAFU/) 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.",
574                "level": 40,
575                "level_name": "WARNING",
576                "name": "audit_input_for",
577                "path": "/measurement-sets/IGVFDS3718PAFU/"
578            }
579        ]
580    },
581    "award": {
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584        "contact_pi": {
585            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
586            "title": "Ansuman Satpathy"
587        },
588        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
589    },
590    "control_for": [],
591    "controlled_access": false,
592    "creation_timestamp": "2025-03-19T20:02:05.711314+00:00",
593    "data_use_limitation_summaries": [
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595    ],
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606        },
607        {
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616        },
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792            ],
793            "content_type": "reads",
794            "controlled_access": false,
795            "creation_timestamp": "2025-03-20T01:10:06.712967+00:00",
796            "file_format": "fastq",
797            "file_size": 5011205397,
798            "href": "/sequence-files/IGVFFI3141LMMO/@@download/IGVFFI3141LMMO.fastq.gz",
799            "s3_uri": "s3://igvf-files/2025/03/20/6d58b187-d016-4eae-99d0-22a31313d0b7/IGVFFI3141LMMO.fastq.gz",
800            "sequencing_platform": {
801                "@id": "/platform-terms/EFO_0008637/",
802                "status": "released",
803                "term_name": "Illumina NovaSeq 6000"
804            },
805            "status": "preview",
806            "submitted_file_name": "Multiome_RNA_X014_G7_L007_P014_S19_L002_R1_001.fastq.gz",
807            "upload_status": "validated"
808        }
809    ],
810    "input_for": [],
811    "lab": {
812        "@id": "/labs/ryan-corces/",
813        "title": "Ryan Corces, Gladstone Institute UCSF"
814    },
815    "multiome_size": 2,
816    "onlist_files": [
817        "/tabular-files/IGVFFI8751YQRY/"
818    ],
819    "onlist_method": "no combination",
820    "preferred_assay_title": "10x multiome",
821    "protocols": [
822        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
823    ],
824    "related_multiome_datasets": [
825        {
826            "@id": "/measurement-sets/IGVFDS5171FIDH/",
827            "accession": "IGVFDS5171FIDH",
828            "status": "preview"
829        }
830    ],
831    "samples": [
832        {
833            "@id": "/multiplexed-samples/IGVFSM3915PNAB/",
834            "@type": [
835                "MultiplexedSample",
836                "Sample",
837                "Item"
838            ],
839            "accession": "IGVFSM3915PNAB",
840            "aliases": [
841                "igvf:corces_multiplexedSample_X014_G7"
842            ],
843            "classifications": [
844                "tissue",
845                "multiplexed sample"
846            ],
847            "disease_terms": [
848                {
849                    "@id": "/phenotype-terms/DOID_14330/",
850                    "status": "in progress",
851                    "term_name": "Parkinson's disease"
852                },
853                {
854                    "@id": "/phenotype-terms/DOID_2377/",
855                    "status": "in progress",
856                    "term_name": "multiple sclerosis"
857                },
858                {
859                    "@id": "/phenotype-terms/DOID_9246/",
860                    "status": "in progress",
861                    "term_name": "cerebral amyloid angiopathy"
862                },
863                {
864                    "@id": "/phenotype-terms/MONDO_0004975/",
865                    "status": "released",
866                    "term_name": "Alzheimer disease"
867                }
868            ],
869            "institutional_certificates": [
870                {
871                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
872                    "certificate_identifier": "IP115-05",
873                    "controlled_access": false,
874                    "status": "in progress"
875                }
876            ],
877            "modifications": [],
878            "sample_terms": [
879                {
880                    "@id": "/sample-terms/UBERON_0001874/",
881                    "@type": [
882                        "SampleTerm",
883                        "OntologyTerm",
884                        "Item"
885                    ],
886                    "status": "preview",
887                    "summary": "putamen",
888                    "term_name": "putamen"
889                },
890                {
891                    "@id": "/sample-terms/UBERON_0002038/",
892                    "@type": [
893                        "SampleTerm",
894                        "OntologyTerm",
895                        "Item"
896                    ],
897                    "status": "preview",
898                    "summary": "substantia nigra",
899                    "term_name": "substantia nigra"
900                },
901                {
902                    "@id": "/sample-terms/UBERON_0002129/",
903                    "@type": [
904                        "SampleTerm",
905                        "OntologyTerm",
906                        "Item"
907                    ],
908                    "status": "preview",
909                    "summary": "cerebellar cortex",
910                    "term_name": "cerebellar cortex"
911                },
912                {
913                    "@id": "/sample-terms/UBERON_0002740/",
914                    "@type": [
915                        "SampleTerm",
916                        "OntologyTerm",
917                        "Item"
918                    ],
919                    "status": "preview",
920                    "summary": "posterior cingulate gyrus",
921                    "term_name": "posterior cingulate gyrus"
922                },
923                {
924                    "@id": "/sample-terms/UBERON_0002771/",
925                    "@type": [
926                        "SampleTerm",
927                        "OntologyTerm",
928                        "Item"
929                    ],
930                    "status": "preview",
931                    "summary": "middle temporal gyrus",
932                    "term_name": "middle temporal gyrus"
933                }
934            ],
935            "status": "preview",
936            "summary": "multiplexed sample: Homo sapiens (male, 89 years) cerebellar cortex tissue; Homo sapiens (male, 80 years) putamen tissue associated with Parkinson's disease; ... and 10 more samples",
937            "taxa": "Homo sapiens",
938            "treatments": []
939        }
940    ],
941    "schema_version": "26",
942    "status": "preview",
943    "submitted_by": {
944        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
945        "title": "Ryan Corces"
946    },
947    "submitted_files_timestamp": "2025-03-20T01:10:00.408184+00:00",
948    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
949    "uuid": "bf95f1e8-bde8-4321-8da7-36a3354ec834"
950}