IGVFDS0082OURJ

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS0082OURJ/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
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10    "aliases": [
11        "igvf:corces_measurementSet_X024_G3_ATAC"
12    ],
13    "assay_term": {
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15        "assay_slims": [
16            "chromatin accessibility"
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18        "status": "released",
19        "term_name": "single-nucleus ATAC-seq"
20    },
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361                "detail": "Preview human donor [IGVFDO6000JDZW](/human-donors/IGVFDO6000JDZW/) has in progress subobject phenotypic feature [a331f60c-ad57-4e67-abef-71ce7f5c533b](/phenotypic-features/a331f60c-ad57-4e67-abef-71ce7f5c533b/).",
362                "level": 30,
363                "level_name": "INTERNAL_ACTION",
364                "name": "audit_item_status",
365                "path": "/human-donors/IGVFDO6000JDZW/"
366            },
367            {
368                "category": "mismatched status",
369                "detail": "Preview human donor [IGVFDO6000JDZW](/human-donors/IGVFDO6000JDZW/) has in progress subobject phenotypic feature [8d33ce55-7875-4008-8ea0-117b359f3bde](/phenotypic-features/8d33ce55-7875-4008-8ea0-117b359f3bde/).",
370                "level": 30,
371                "level_name": "INTERNAL_ACTION",
372                "name": "audit_item_status",
373                "path": "/human-donors/IGVFDO6000JDZW/"
374            },
375            {
376                "category": "mismatched status",
377                "detail": "Preview human donor [IGVFDO6000JDZW](/human-donors/IGVFDO6000JDZW/) has in progress subobject phenotypic feature [e5d45886-2d5a-4f54-9595-ddecf9ee0dc3](/phenotypic-features/e5d45886-2d5a-4f54-9595-ddecf9ee0dc3/).",
378                "level": 30,
379                "level_name": "INTERNAL_ACTION",
380                "name": "audit_item_status",
381                "path": "/human-donors/IGVFDO6000JDZW/"
382            },
383            {
384                "category": "mismatched status",
385                "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/).",
386                "level": 30,
387                "level_name": "INTERNAL_ACTION",
388                "name": "audit_item_status",
389                "path": "/human-donors/IGVFDO0565OSFT/"
390            },
391            {
392                "category": "mismatched status",
393                "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/).",
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 [8873c4a9-e724-443a-a05e-06e9e0b589d5](/phenotypic-features/8873c4a9-e724-443a-a05e-06e9e0b589d5/).",
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 [e4a3f50a-af00-468e-a649-00d00f9509fa](/phenotypic-features/e4a3f50a-af00-468e-a649-00d00f9509fa/).",
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 [a0192d92-603a-484a-9f0f-36150134dec4](/phenotypic-features/a0192d92-603a-484a-9f0f-36150134dec4/).",
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 [15a2db58-5d04-4278-9bcf-bbb6923e95b2](/phenotypic-features/15a2db58-5d04-4278-9bcf-bbb6923e95b2/).",
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 [IGVFDO7306YMGC](/human-donors/IGVFDO7306YMGC/) has in progress subobject phenotypic feature [c2d841ed-9a79-4029-8f19-938166bb96ee](/phenotypic-features/c2d841ed-9a79-4029-8f19-938166bb96ee/).",
434                "level": 30,
435                "level_name": "INTERNAL_ACTION",
436                "name": "audit_item_status",
437                "path": "/human-donors/IGVFDO7306YMGC/"
438            },
439            {
440                "category": "mismatched status",
441                "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/).",
442                "level": 30,
443                "level_name": "INTERNAL_ACTION",
444                "name": "audit_item_status",
445                "path": "/human-donors/IGVFDO7306YMGC/"
446            },
447            {
448                "category": "mismatched status",
449                "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/).",
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 [b7d1671f-0cb9-42ce-84bf-70d7508a2dc8](/phenotypic-features/b7d1671f-0cb9-42ce-84bf-70d7508a2dc8/).",
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 [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [687e8b69-25f0-4bb5-969e-635dd2d3f4a5](/phenotypic-features/687e8b69-25f0-4bb5-969e-635dd2d3f4a5/).",
474                "level": 30,
475                "level_name": "INTERNAL_ACTION",
476                "name": "audit_item_status",
477                "path": "/human-donors/IGVFDO4438WASY/"
478            },
479            {
480                "category": "mismatched status",
481                "detail": "Preview human donor [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [a307f67e-a27c-4f71-933b-8391d36a0ffc](/phenotypic-features/a307f67e-a27c-4f71-933b-8391d36a0ffc/).",
482                "level": 30,
483                "level_name": "INTERNAL_ACTION",
484                "name": "audit_item_status",
485                "path": "/human-donors/IGVFDO4438WASY/"
486            },
487            {
488                "category": "mismatched status",
489                "detail": "Preview human donor [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [c720825e-ee74-4c36-8a5e-9c70924435be](/phenotypic-features/c720825e-ee74-4c36-8a5e-9c70924435be/).",
490                "level": 30,
491                "level_name": "INTERNAL_ACTION",
492                "name": "audit_item_status",
493                "path": "/human-donors/IGVFDO4438WASY/"
494            },
495            {
496                "category": "mismatched status",
497                "detail": "Preview human donor [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [9c586031-f537-409b-8205-585a19621b3f](/phenotypic-features/9c586031-f537-409b-8205-585a19621b3f/).",
498                "level": 30,
499                "level_name": "INTERNAL_ACTION",
500                "name": "audit_item_status",
501                "path": "/human-donors/IGVFDO4438WASY/"
502            },
503            {
504                "category": "mismatched status",
505                "detail": "Preview human donor [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [f6830b8c-bd31-4ecc-868b-9167f991411f](/phenotypic-features/f6830b8c-bd31-4ecc-868b-9167f991411f/).",
506                "level": 30,
507                "level_name": "INTERNAL_ACTION",
508                "name": "audit_item_status",
509                "path": "/human-donors/IGVFDO4438WASY/"
510            },
511            {
512                "category": "mismatched status",
513                "detail": "Preview human donor [IGVFDO4438WASY](/human-donors/IGVFDO4438WASY/) has in progress subobject phenotypic feature [1e832ff1-71d0-41fc-9f36-fd4498dfee00](/phenotypic-features/1e832ff1-71d0-41fc-9f36-fd4498dfee00/).",
514                "level": 30,
515                "level_name": "INTERNAL_ACTION",
516                "name": "audit_item_status",
517                "path": "/human-donors/IGVFDO4438WASY/"
518            },
519            {
520                "category": "mismatched status",
521                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [6996673c-1993-4682-87ae-6d3968ab4eba](/phenotypic-features/6996673c-1993-4682-87ae-6d3968ab4eba/).",
522                "level": 30,
523                "level_name": "INTERNAL_ACTION",
524                "name": "audit_item_status",
525                "path": "/human-donors/IGVFDO3911JQLE/"
526            },
527            {
528                "category": "mismatched status",
529                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [de15fdf8-d7dc-4a9e-9fcd-d5bc83119b19](/phenotypic-features/de15fdf8-d7dc-4a9e-9fcd-d5bc83119b19/).",
530                "level": 30,
531                "level_name": "INTERNAL_ACTION",
532                "name": "audit_item_status",
533                "path": "/human-donors/IGVFDO3911JQLE/"
534            },
535            {
536                "category": "mismatched status",
537                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [201dcd5e-a9ec-49ae-88a5-7f5f59f4d6dc](/phenotypic-features/201dcd5e-a9ec-49ae-88a5-7f5f59f4d6dc/).",
538                "level": 30,
539                "level_name": "INTERNAL_ACTION",
540                "name": "audit_item_status",
541                "path": "/human-donors/IGVFDO3911JQLE/"
542            },
543            {
544                "category": "mismatched status",
545                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [33c7729b-5ddf-4b58-bd09-9717dac5eb61](/phenotypic-features/33c7729b-5ddf-4b58-bd09-9717dac5eb61/).",
546                "level": 30,
547                "level_name": "INTERNAL_ACTION",
548                "name": "audit_item_status",
549                "path": "/human-donors/IGVFDO3911JQLE/"
550            },
551            {
552                "category": "mismatched status",
553                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [7007fd27-1b94-42fb-a2cb-5a579dcbbfc2](/phenotypic-features/7007fd27-1b94-42fb-a2cb-5a579dcbbfc2/).",
554                "level": 30,
555                "level_name": "INTERNAL_ACTION",
556                "name": "audit_item_status",
557                "path": "/human-donors/IGVFDO3911JQLE/"
558            },
559            {
560                "category": "mismatched status",
561                "detail": "Preview human donor [IGVFDO3911JQLE](/human-donors/IGVFDO3911JQLE/) has in progress subobject phenotypic feature [2770d2df-cfa4-4078-9bd1-51ee1d3c62b4](/phenotypic-features/2770d2df-cfa4-4078-9bd1-51ee1d3c62b4/).",
562                "level": 30,
563                "level_name": "INTERNAL_ACTION",
564                "name": "audit_item_status",
565                "path": "/human-donors/IGVFDO3911JQLE/"
566            }
567        ],
568        "NOT_COMPLIANT": [
569            {
570                "category": "missing sequence specification",
571                "detail": "Measurement set [IGVFDS0082OURJ](/measurement-sets/IGVFDS0082OURJ/) has sequence file(s): [IGVFFI6731IYIZ](/sequence-files/IGVFFI6731IYIZ/), [IGVFFI0950UYQV](/sequence-files/IGVFFI0950UYQV/), [IGVFFI6588RZPT](/sequence-files/IGVFFI6588RZPT/), [IGVFFI2191ELUA](/sequence-files/IGVFFI2191ELUA/) 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.",
572                "level": 50,
573                "level_name": "NOT_COMPLIANT",
574                "name": "audit_missing_seqspec",
575                "path": "/measurement-sets/IGVFDS0082OURJ/"
576            },
577            {
578                "category": "missing strand specificity",
579                "detail": "Measurement set [IGVFDS0082OURJ](/measurement-sets/IGVFDS0082OURJ/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
580                "level": 50,
581                "level_name": "NOT_COMPLIANT",
582                "name": "audit_missing_strand_specificity",
583                "path": "/measurement-sets/IGVFDS0082OURJ/"
584            }
585        ],
586        "WARNING": [
587            {
588                "category": "missing analysis",
589                "detail": "Measurement set [IGVFDS0082OURJ](/measurement-sets/IGVFDS0082OURJ/) 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.",
590                "level": 40,
591                "level_name": "WARNING",
592                "name": "audit_input_for",
593                "path": "/measurement-sets/IGVFDS0082OURJ/"
594            }
595        ]
596    },
597    "award": {
598        "@id": "/awards/HG012076/",
599        "component": "mapping",
600        "contact_pi": {
601            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
602            "title": "Ansuman Satpathy"
603        },
604        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
605    },
606    "control_for": [],
607    "controlled_access": false,
608    "creation_timestamp": "2025-03-19T19:41:47.905075+00:00",
609    "data_use_limitation_summaries": [
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611    ],
612    "donors": [
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615            "accession": "IGVFDO7095OCLJ",
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618            ],
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620            "status": "preview",
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622        },
623        {
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625            "accession": "IGVFDO7606UOXI",
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628            ],
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631            "taxa": "Homo sapiens"
632        },
633        {
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635            "accession": "IGVFDO4108VCBA",
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683        {
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693        {
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713        {
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781        {
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785                "igvf:corces_sequenceFile_ATAC_X024_G3_P023_L003_R2"
786            ],
787            "content_type": "reads",
788            "controlled_access": false,
789            "creation_timestamp": "2025-03-20T01:41:32.111864+00:00",
790            "file_format": "fastq",
791            "file_size": 3892397294,
792            "href": "/sequence-files/IGVFFI6588RZPT/@@download/IGVFFI6588RZPT.fastq.gz",
793            "s3_uri": "s3://igvf-files/2025/03/20/a5879057-02b4-4246-a9ce-7274dee869b4/IGVFFI6588RZPT.fastq.gz",
794            "sequencing_platform": {
795                "@id": "/platform-terms/EFO_0008637/",
796                "status": "released",
797                "term_name": "Illumina NovaSeq 6000"
798            },
799            "status": "preview",
800            "submitted_file_name": "Multiome_ATAC_X024_G3_L003_P023_S27_L003_R2_001.fastq.gz",
801            "upload_status": "validated"
802        },
803        {
804            "@id": "/sequence-files/IGVFFI2191ELUA/",
805            "accession": "IGVFFI2191ELUA",
806            "aliases": [
807                "igvf:corces_sequenceFile_ATAC_X024_G3_P023_L003_R1"
808            ],
809            "content_type": "reads",
810            "controlled_access": false,
811            "creation_timestamp": "2025-03-20T01:41:28.152609+00:00",
812            "file_format": "fastq",
813            "file_size": 7106150272,
814            "href": "/sequence-files/IGVFFI2191ELUA/@@download/IGVFFI2191ELUA.fastq.gz",
815            "s3_uri": "s3://igvf-files/2025/03/20/49275213-6e5f-42c1-835b-6a8aa41d98e6/IGVFFI2191ELUA.fastq.gz",
816            "sequencing_platform": {
817                "@id": "/platform-terms/EFO_0008637/",
818                "status": "released",
819                "term_name": "Illumina NovaSeq 6000"
820            },
821            "status": "preview",
822            "submitted_file_name": "Multiome_ATAC_X024_G3_L003_P023_S27_L003_R1_001.fastq.gz",
823            "upload_status": "validated"
824        }
825    ],
826    "input_for": [],
827    "lab": {
828        "@id": "/labs/ryan-corces/",
829        "title": "Ryan Corces, Gladstone Institute UCSF"
830    },
831    "multiome_size": 2,
832    "onlist_files": [
833        "/tabular-files/IGVFFI7587TJLC/"
834    ],
835    "onlist_method": "no combination",
836    "preferred_assay_title": "10x multiome",
837    "protocols": [
838        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
839    ],
840    "related_multiome_datasets": [
841        {
842            "@id": "/measurement-sets/IGVFDS6602VADR/",
843            "accession": "IGVFDS6602VADR",
844            "status": "preview"
845        }
846    ],
847    "samples": [
848        {
849            "@id": "/multiplexed-samples/IGVFSM7556QXIA/",
850            "@type": [
851                "MultiplexedSample",
852                "Sample",
853                "Item"
854            ],
855            "accession": "IGVFSM7556QXIA",
856            "aliases": [
857                "igvf:corces_multiplexedSample_X024_G3"
858            ],
859            "classifications": [
860                "tissue",
861                "multiplexed sample"
862            ],
863            "disease_terms": [
864                {
865                    "@id": "/phenotype-terms/DOID_0080832/",
866                    "status": "in progress",
867                    "term_name": "mild cognitive impairment"
868                },
869                {
870                    "@id": "/phenotype-terms/DOID_14330/",
871                    "status": "in progress",
872                    "term_name": "Parkinson's disease"
873                },
874                {
875                    "@id": "/phenotype-terms/DOID_9246/",
876                    "status": "in progress",
877                    "term_name": "cerebral amyloid angiopathy"
878                }
879            ],
880            "institutional_certificates": [
881                {
882                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
883                    "certificate_identifier": "IP115-05",
884                    "controlled_access": false,
885                    "status": "in progress"
886                }
887            ],
888            "modifications": [],
889            "sample_terms": [
890                {
891                    "@id": "/sample-terms/UBERON_0001874/",
892                    "@type": [
893                        "SampleTerm",
894                        "OntologyTerm",
895                        "Item"
896                    ],
897                    "status": "preview",
898                    "summary": "putamen",
899                    "term_name": "putamen"
900                },
901                {
902                    "@id": "/sample-terms/UBERON_0002038/",
903                    "@type": [
904                        "SampleTerm",
905                        "OntologyTerm",
906                        "Item"
907                    ],
908                    "status": "preview",
909                    "summary": "substantia nigra",
910                    "term_name": "substantia nigra"
911                },
912                {
913                    "@id": "/sample-terms/UBERON_0002129/",
914                    "@type": [
915                        "SampleTerm",
916                        "OntologyTerm",
917                        "Item"
918                    ],
919                    "status": "preview",
920                    "summary": "cerebellar cortex",
921                    "term_name": "cerebellar cortex"
922                },
923                {
924                    "@id": "/sample-terms/UBERON_0002740/",
925                    "@type": [
926                        "SampleTerm",
927                        "OntologyTerm",
928                        "Item"
929                    ],
930                    "status": "preview",
931                    "summary": "posterior cingulate gyrus",
932                    "term_name": "posterior cingulate gyrus"
933                },
934                {
935                    "@id": "/sample-terms/UBERON_0002771/",
936                    "@type": [
937                        "SampleTerm",
938                        "OntologyTerm",
939                        "Item"
940                    ],
941                    "status": "preview",
942                    "summary": "middle temporal gyrus",
943                    "term_name": "middle temporal gyrus"
944                }
945            ],
946            "status": "preview",
947            "summary": "multiplexed sample: Homo sapiens (male, 78 years) cerebellar cortex tissue associated with Parkinson's disease; Homo sapiens (male, 75 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 10 more samples",
948            "taxa": "Homo sapiens",
949            "treatments": []
950        }
951    ],
952    "schema_version": "26",
953    "status": "preview",
954    "submitted_by": {
955        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
956        "title": "Ryan Corces"
957    },
958    "submitted_files_timestamp": "2025-03-20T01:41:24.821996+00:00",
959    "summary": "single-nucleus ATAC-seq (10x multiome)",
960    "uuid": "cbf40a91-654c-4735-8df9-b5329f8c7aa3"
961}