IGVFDS0226WYES

1{
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10    "aliases": [
11        "igvf:corces_measurementSet_X009_G8_ATAC"
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15        "assay_slims": [
16            "chromatin accessibility"
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18        "status": "released",
19        "term_name": "single-nucleus ATAC-seq"
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359            {
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361                "detail": "Preview human donor [IGVFDO3471KCPD](/human-donors/IGVFDO3471KCPD/) has in progress subobject phenotypic feature [7cef33e4-2883-4036-9171-f05b4ad41d82](/phenotypic-features/7cef33e4-2883-4036-9171-f05b4ad41d82/).",
362                "level": 30,
363                "level_name": "INTERNAL_ACTION",
364                "name": "audit_item_status",
365                "path": "/human-donors/IGVFDO3471KCPD/"
366            },
367            {
368                "category": "mismatched status",
369                "detail": "Preview human donor [IGVFDO3471KCPD](/human-donors/IGVFDO3471KCPD/) has in progress subobject phenotypic feature [ce38b3de-52ef-4922-90a9-554f69f41f83](/phenotypic-features/ce38b3de-52ef-4922-90a9-554f69f41f83/).",
370                "level": 30,
371                "level_name": "INTERNAL_ACTION",
372                "name": "audit_item_status",
373                "path": "/human-donors/IGVFDO3471KCPD/"
374            },
375            {
376                "category": "mismatched status",
377                "detail": "Preview human donor [IGVFDO3471KCPD](/human-donors/IGVFDO3471KCPD/) has in progress subobject phenotypic feature [bf330bc2-8a2a-4dc7-8aeb-f572a5fe9f1d](/phenotypic-features/bf330bc2-8a2a-4dc7-8aeb-f572a5fe9f1d/).",
378                "level": 30,
379                "level_name": "INTERNAL_ACTION",
380                "name": "audit_item_status",
381                "path": "/human-donors/IGVFDO3471KCPD/"
382            },
383            {
384                "category": "mismatched status",
385                "detail": "Preview human donor [IGVFDO3471KCPD](/human-donors/IGVFDO3471KCPD/) has in progress subobject phenotypic feature [63252125-58f4-4e29-91f3-4103a1645797](/phenotypic-features/63252125-58f4-4e29-91f3-4103a1645797/).",
386                "level": 30,
387                "level_name": "INTERNAL_ACTION",
388                "name": "audit_item_status",
389                "path": "/human-donors/IGVFDO3471KCPD/"
390            },
391            {
392                "category": "mismatched status",
393                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [a0192d92-603a-484a-9f0f-36150134dec4](/phenotypic-features/a0192d92-603a-484a-9f0f-36150134dec4/).",
394                "level": 30,
395                "level_name": "INTERNAL_ACTION",
396                "name": "audit_item_status",
397                "path": "/human-donors/IGVFDO0565OSFT/"
398            },
399            {
400                "category": "mismatched status",
401                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [15a2db58-5d04-4278-9bcf-bbb6923e95b2](/phenotypic-features/15a2db58-5d04-4278-9bcf-bbb6923e95b2/).",
402                "level": 30,
403                "level_name": "INTERNAL_ACTION",
404                "name": "audit_item_status",
405                "path": "/human-donors/IGVFDO0565OSFT/"
406            },
407            {
408                "category": "mismatched status",
409                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [4d73651a-95b0-453f-bf9e-85a83965b18b](/phenotypic-features/4d73651a-95b0-453f-bf9e-85a83965b18b/).",
410                "level": 30,
411                "level_name": "INTERNAL_ACTION",
412                "name": "audit_item_status",
413                "path": "/human-donors/IGVFDO0565OSFT/"
414            },
415            {
416                "category": "mismatched status",
417                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [e4a3f50a-af00-468e-a649-00d00f9509fa](/phenotypic-features/e4a3f50a-af00-468e-a649-00d00f9509fa/).",
418                "level": 30,
419                "level_name": "INTERNAL_ACTION",
420                "name": "audit_item_status",
421                "path": "/human-donors/IGVFDO0565OSFT/"
422            },
423            {
424                "category": "mismatched status",
425                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [8873c4a9-e724-443a-a05e-06e9e0b589d5](/phenotypic-features/8873c4a9-e724-443a-a05e-06e9e0b589d5/).",
426                "level": 30,
427                "level_name": "INTERNAL_ACTION",
428                "name": "audit_item_status",
429                "path": "/human-donors/IGVFDO0565OSFT/"
430            },
431            {
432                "category": "mismatched status",
433                "detail": "Preview human donor [IGVFDO0565OSFT](/human-donors/IGVFDO0565OSFT/) has in progress subobject phenotypic feature [cc4f681e-74b9-4639-96f4-47f5c05c6ff2](/phenotypic-features/cc4f681e-74b9-4639-96f4-47f5c05c6ff2/).",
434                "level": 30,
435                "level_name": "INTERNAL_ACTION",
436                "name": "audit_item_status",
437                "path": "/human-donors/IGVFDO0565OSFT/"
438            },
439            {
440                "category": "mismatched status",
441                "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/).",
442                "level": 30,
443                "level_name": "INTERNAL_ACTION",
444                "name": "audit_item_status",
445                "path": "/human-donors/IGVFDO3971UIZC/"
446            },
447            {
448                "category": "mismatched status",
449                "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/).",
450                "level": 30,
451                "level_name": "INTERNAL_ACTION",
452                "name": "audit_item_status",
453                "path": "/human-donors/IGVFDO3971UIZC/"
454            },
455            {
456                "category": "mismatched status",
457                "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/).",
458                "level": 30,
459                "level_name": "INTERNAL_ACTION",
460                "name": "audit_item_status",
461                "path": "/human-donors/IGVFDO3971UIZC/"
462            },
463            {
464                "category": "mismatched status",
465                "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/).",
466                "level": 30,
467                "level_name": "INTERNAL_ACTION",
468                "name": "audit_item_status",
469                "path": "/human-donors/IGVFDO3971UIZC/"
470            },
471            {
472                "category": "mismatched status",
473                "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/).",
474                "level": 30,
475                "level_name": "INTERNAL_ACTION",
476                "name": "audit_item_status",
477                "path": "/human-donors/IGVFDO3971UIZC/"
478            },
479            {
480                "category": "mismatched status",
481                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [08889386-b912-4c98-bab0-a34b9d17b94b](/phenotypic-features/08889386-b912-4c98-bab0-a34b9d17b94b/).",
482                "level": 30,
483                "level_name": "INTERNAL_ACTION",
484                "name": "audit_item_status",
485                "path": "/human-donors/IGVFDO2045AFUW/"
486            },
487            {
488                "category": "mismatched status",
489                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [f09ab874-d34c-4112-a29b-df214539e6d3](/phenotypic-features/f09ab874-d34c-4112-a29b-df214539e6d3/).",
490                "level": 30,
491                "level_name": "INTERNAL_ACTION",
492                "name": "audit_item_status",
493                "path": "/human-donors/IGVFDO2045AFUW/"
494            },
495            {
496                "category": "mismatched status",
497                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [c1a58f29-abf8-4622-8885-66a6a187bb34](/phenotypic-features/c1a58f29-abf8-4622-8885-66a6a187bb34/).",
498                "level": 30,
499                "level_name": "INTERNAL_ACTION",
500                "name": "audit_item_status",
501                "path": "/human-donors/IGVFDO2045AFUW/"
502            },
503            {
504                "category": "mismatched status",
505                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [d5751e04-de2d-45d7-87a7-92a56d3bf07a](/phenotypic-features/d5751e04-de2d-45d7-87a7-92a56d3bf07a/).",
506                "level": 30,
507                "level_name": "INTERNAL_ACTION",
508                "name": "audit_item_status",
509                "path": "/human-donors/IGVFDO2045AFUW/"
510            },
511            {
512                "category": "mismatched status",
513                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [c6cfcb7d-d869-4c3a-a1ba-29a4ce9dd0c8](/phenotypic-features/c6cfcb7d-d869-4c3a-a1ba-29a4ce9dd0c8/).",
514                "level": 30,
515                "level_name": "INTERNAL_ACTION",
516                "name": "audit_item_status",
517                "path": "/human-donors/IGVFDO2045AFUW/"
518            },
519            {
520                "category": "mismatched status",
521                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [894b8828-e989-4019-811a-f7d4fde1ec70](/phenotypic-features/894b8828-e989-4019-811a-f7d4fde1ec70/).",
522                "level": 30,
523                "level_name": "INTERNAL_ACTION",
524                "name": "audit_item_status",
525                "path": "/human-donors/IGVFDO2045AFUW/"
526            }
527        ],
528        "NOT_COMPLIANT": [
529            {
530                "category": "missing sequence specification",
531                "detail": "Measurement set [IGVFDS0226WYES](/measurement-sets/IGVFDS0226WYES/) has sequence file(s): [IGVFFI0697WBEY](/sequence-files/IGVFFI0697WBEY/), [IGVFFI6379DSJK](/sequence-files/IGVFFI6379DSJK/), [IGVFFI1610KSWN](/sequence-files/IGVFFI1610KSWN/), [IGVFFI4631KWSC](/sequence-files/IGVFFI4631KWSC/) 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/IGVFDS0226WYES/"
536            },
537            {
538                "category": "missing strand specificity",
539                "detail": "Measurement set [IGVFDS0226WYES](/measurement-sets/IGVFDS0226WYES/) 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/IGVFDS0226WYES/"
544            }
545        ],
546        "WARNING": [
547            {
548                "category": "missing analysis",
549                "detail": "Measurement set [IGVFDS0226WYES](/measurement-sets/IGVFDS0226WYES/) 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/IGVFDS0226WYES/"
554            }
555        ]
556    },
557    "award": {
558        "@id": "/awards/HG012076/",
559        "component": "mapping",
560        "contact_pi": {
561            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
562            "title": "Ansuman Satpathy"
563        },
564        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
565    },
566    "control_for": [],
567    "controlled_access": false,
568    "creation_timestamp": "2025-03-19T19:38:30.926087+00:00",
569    "data_use_limitation_summaries": [
570        "No limitations"
571    ],
572    "donors": [
573        {
574            "@id": "/human-donors/IGVFDO8891KXRJ/",
575            "accession": "IGVFDO8891KXRJ",
576            "aliases": [
577                "igvf:corces_donor_BANN1737"
578            ],
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580            "status": "preview",
581            "taxa": "Homo sapiens"
582        },
583        {
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585            "accession": "IGVFDO3317CNEB",
586            "aliases": [
587                "igvf:corces_donor_BANN1902"
588            ],
589            "sex": "male",
590            "status": "preview",
591            "taxa": "Homo sapiens"
592        },
593        {
594            "@id": "/human-donors/IGVFDO2127ZJPS/",
595            "accession": "IGVFDO2127ZJPS",
596            "aliases": [
597                "igvf:corces_donor_BANN1560"
598            ],
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600            "status": "preview",
601            "taxa": "Homo sapiens"
602        },
603        {
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605            "accession": "IGVFDO1464XWYC",
606            "aliases": [
607                "igvf:corces_donor_BANN1809"
608            ],
609            "sex": "male",
610            "status": "preview",
611            "taxa": "Homo sapiens"
612        },
613        {
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615            "accession": "IGVFDO2045AFUW",
616            "aliases": [
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618            ],
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620            "status": "preview",
621            "taxa": "Homo sapiens"
622        },
623        {
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625            "accession": "IGVFDO7306YMGC",
626            "aliases": [
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628            ],
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630            "status": "preview",
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632        },
633        {
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635            "accession": "IGVFDO2848YHMH",
636            "aliases": [
637                "igvf:corces_donor_BANN2038"
638            ],
639            "sex": "male",
640            "status": "preview",
641            "taxa": "Homo sapiens"
642        },
643        {
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645            "accession": "IGVFDO3911JQLE",
646            "aliases": [
647                "igvf:corces_donor_BANN1412"
648            ],
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650            "status": "preview",
651            "taxa": "Homo sapiens"
652        },
653        {
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655            "accession": "IGVFDO0565OSFT",
656            "aliases": [
657                "igvf:corces_donor_BANN1805"
658            ],
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660            "status": "preview",
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662        },
663        {
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665            "accession": "IGVFDO3971UIZC",
666            "aliases": [
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672        },
673        {
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676            "aliases": [
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682        },
683        {
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687                "igvf:corces_donor_BANN1647"
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735                "term_name": "Illumina NovaSeq 6000"
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754            "sequencing_platform": {
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757                "term_name": "Illumina NovaSeq 6000"
758            },
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760            "submitted_file_name": "Multiome_ATAC_X009_G8_L008_P007_S28_L003_I1_001.fastq.gz",
761            "upload_status": "validated"
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763        {
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765            "accession": "IGVFFI4631KWSC",
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770            "controlled_access": false,
771            "creation_timestamp": "2025-03-20T00:46:33.981805+00:00",
772            "file_format": "fastq",
773            "file_size": 9762822297,
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777                "@id": "/platform-terms/EFO_0008637/",
778                "status": "released",
779                "term_name": "Illumina NovaSeq 6000"
780            },
781            "status": "preview",
782            "submitted_file_name": "Multiome_ATAC_X009_G8_L008_P007_S28_L003_R3_001.fastq.gz",
783            "upload_status": "validated"
784        }
785    ],
786    "input_for": [],
787    "lab": {
788        "@id": "/labs/ryan-corces/",
789        "title": "Ryan Corces, Gladstone Institute UCSF"
790    },
791    "multiome_size": 2,
792    "onlist_files": [
793        "/tabular-files/IGVFFI7587TJLC/"
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/IGVFDS4072OFXV/",
803            "accession": "IGVFDS4072OFXV",
804            "status": "preview"
805        }
806    ],
807    "samples": [
808        {
809            "@id": "/multiplexed-samples/IGVFSM5614IWFO/",
810            "@type": [
811                "MultiplexedSample",
812                "Sample",
813                "Item"
814            ],
815            "accession": "IGVFSM5614IWFO",
816            "aliases": [
817                "igvf:corces_multiplexedSample_X009_G8"
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": "2025-03-20T00:46:26.268097+00:00",
919    "summary": "single-nucleus ATAC-seq (10x multiome)",
920    "uuid": "0a910e0f-798a-4a7c-9a6f-12d27c5b9663"
921}