IGVFDS3520MQEA

1{
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3    "@id": "/measurement-sets/IGVFDS3520MQEA/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS3520MQEA",
10    "aliases": [
11        "igvf:corces_measurementSet_X036_G5_ATAC"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0002762/",
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 [IGVFDO2031ESZX](/human-donors/IGVFDO2031ESZX/) has in progress subobject phenotypic feature [e4956f7b-f7c0-4081-a17f-b98bace43aac](/phenotypic-features/e4956f7b-f7c0-4081-a17f-b98bace43aac/).",
362                "level": 30,
363                "level_name": "INTERNAL_ACTION",
364                "name": "audit_item_status",
365                "path": "/human-donors/IGVFDO2031ESZX/"
366            },
367            {
368                "category": "mismatched status",
369                "detail": "Preview human donor [IGVFDO2031ESZX](/human-donors/IGVFDO2031ESZX/) has in progress subobject phenotypic feature [db023dab-98aa-456b-b675-32fe8cb67884](/phenotypic-features/db023dab-98aa-456b-b675-32fe8cb67884/).",
370                "level": 30,
371                "level_name": "INTERNAL_ACTION",
372                "name": "audit_item_status",
373                "path": "/human-donors/IGVFDO2031ESZX/"
374            },
375            {
376                "category": "mismatched status",
377                "detail": "Preview human donor [IGVFDO7095OCLJ](/human-donors/IGVFDO7095OCLJ/) has in progress subobject phenotypic feature [e479b054-101b-4494-9188-68e22dbfb4a7](/phenotypic-features/e479b054-101b-4494-9188-68e22dbfb4a7/).",
378                "level": 30,
379                "level_name": "INTERNAL_ACTION",
380                "name": "audit_item_status",
381                "path": "/human-donors/IGVFDO7095OCLJ/"
382            },
383            {
384                "category": "mismatched status",
385                "detail": "Preview human donor [IGVFDO7095OCLJ](/human-donors/IGVFDO7095OCLJ/) has in progress subobject phenotypic feature [8363461a-620b-4625-8cd0-fe83928b21f7](/phenotypic-features/8363461a-620b-4625-8cd0-fe83928b21f7/).",
386                "level": 30,
387                "level_name": "INTERNAL_ACTION",
388                "name": "audit_item_status",
389                "path": "/human-donors/IGVFDO7095OCLJ/"
390            },
391            {
392                "category": "mismatched status",
393                "detail": "Preview human donor [IGVFDO7095OCLJ](/human-donors/IGVFDO7095OCLJ/) has in progress subobject phenotypic feature [ac242806-2b11-40d0-9628-6e319c7d67b6](/phenotypic-features/ac242806-2b11-40d0-9628-6e319c7d67b6/).",
394                "level": 30,
395                "level_name": "INTERNAL_ACTION",
396                "name": "audit_item_status",
397                "path": "/human-donors/IGVFDO7095OCLJ/"
398            },
399            {
400                "category": "mismatched status",
401                "detail": "Preview human donor [IGVFDO7095OCLJ](/human-donors/IGVFDO7095OCLJ/) has in progress subobject phenotypic feature [9f57f492-c482-4a53-8922-5ec40bf8777f](/phenotypic-features/9f57f492-c482-4a53-8922-5ec40bf8777f/).",
402                "level": 30,
403                "level_name": "INTERNAL_ACTION",
404                "name": "audit_item_status",
405                "path": "/human-donors/IGVFDO7095OCLJ/"
406            },
407            {
408                "category": "mismatched status",
409                "detail": "Preview human donor [IGVFDO7095OCLJ](/human-donors/IGVFDO7095OCLJ/) has in progress subobject phenotypic feature [44805391-bb84-4aee-b329-cffefc4119ce](/phenotypic-features/44805391-bb84-4aee-b329-cffefc4119ce/).",
410                "level": 30,
411                "level_name": "INTERNAL_ACTION",
412                "name": "audit_item_status",
413                "path": "/human-donors/IGVFDO7095OCLJ/"
414            },
415            {
416                "category": "mismatched status",
417                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [f4679a5f-a8ec-409d-b8fe-b1b20f27d207](/phenotypic-features/f4679a5f-a8ec-409d-b8fe-b1b20f27d207/).",
418                "level": 30,
419                "level_name": "INTERNAL_ACTION",
420                "name": "audit_item_status",
421                "path": "/human-donors/IGVFDO7720JNYZ/"
422            },
423            {
424                "category": "mismatched status",
425                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [d7589c14-ec5a-4631-8fa0-e2d6776dab9b](/phenotypic-features/d7589c14-ec5a-4631-8fa0-e2d6776dab9b/).",
426                "level": 30,
427                "level_name": "INTERNAL_ACTION",
428                "name": "audit_item_status",
429                "path": "/human-donors/IGVFDO7720JNYZ/"
430            },
431            {
432                "category": "mismatched status",
433                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [b8d2bdc8-6429-461f-b00d-b530a631c5a5](/phenotypic-features/b8d2bdc8-6429-461f-b00d-b530a631c5a5/).",
434                "level": 30,
435                "level_name": "INTERNAL_ACTION",
436                "name": "audit_item_status",
437                "path": "/human-donors/IGVFDO7720JNYZ/"
438            },
439            {
440                "category": "mismatched status",
441                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [4cf206b1-67ce-4e84-9858-add2a84e81f2](/phenotypic-features/4cf206b1-67ce-4e84-9858-add2a84e81f2/).",
442                "level": 30,
443                "level_name": "INTERNAL_ACTION",
444                "name": "audit_item_status",
445                "path": "/human-donors/IGVFDO7720JNYZ/"
446            },
447            {
448                "category": "mismatched status",
449                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [86df8b53-cb57-4e34-83a6-c8cf66b85450](/phenotypic-features/86df8b53-cb57-4e34-83a6-c8cf66b85450/).",
450                "level": 30,
451                "level_name": "INTERNAL_ACTION",
452                "name": "audit_item_status",
453                "path": "/human-donors/IGVFDO7720JNYZ/"
454            },
455            {
456                "category": "mismatched status",
457                "detail": "Preview human donor [IGVFDO7720JNYZ](/human-donors/IGVFDO7720JNYZ/) has in progress subobject phenotypic feature [e21c1b8a-f7fb-4412-93a3-00f24d6280ac](/phenotypic-features/e21c1b8a-f7fb-4412-93a3-00f24d6280ac/).",
458                "level": 30,
459                "level_name": "INTERNAL_ACTION",
460                "name": "audit_item_status",
461                "path": "/human-donors/IGVFDO7720JNYZ/"
462            },
463            {
464                "category": "mismatched status",
465                "detail": "Preview human donor [IGVFDO8547HLIG](/human-donors/IGVFDO8547HLIG/) has in progress subobject phenotypic feature [5bcd89ab-19d5-4404-be57-fb619f69d42a](/phenotypic-features/5bcd89ab-19d5-4404-be57-fb619f69d42a/).",
466                "level": 30,
467                "level_name": "INTERNAL_ACTION",
468                "name": "audit_item_status",
469                "path": "/human-donors/IGVFDO8547HLIG/"
470            },
471            {
472                "category": "mismatched status",
473                "detail": "Preview human donor [IGVFDO8547HLIG](/human-donors/IGVFDO8547HLIG/) has in progress subobject phenotypic feature [9afbbb32-aec3-415c-9550-be4507e4a552](/phenotypic-features/9afbbb32-aec3-415c-9550-be4507e4a552/).",
474                "level": 30,
475                "level_name": "INTERNAL_ACTION",
476                "name": "audit_item_status",
477                "path": "/human-donors/IGVFDO8547HLIG/"
478            },
479            {
480                "category": "mismatched status",
481                "detail": "Preview human donor [IGVFDO8547HLIG](/human-donors/IGVFDO8547HLIG/) has in progress subobject phenotypic feature [d828635f-bd01-4b73-87de-10d233d81028](/phenotypic-features/d828635f-bd01-4b73-87de-10d233d81028/).",
482                "level": 30,
483                "level_name": "INTERNAL_ACTION",
484                "name": "audit_item_status",
485                "path": "/human-donors/IGVFDO8547HLIG/"
486            },
487            {
488                "category": "mismatched status",
489                "detail": "Preview human donor [IGVFDO8547HLIG](/human-donors/IGVFDO8547HLIG/) has in progress subobject phenotypic feature [edbac599-10a4-47e7-b223-454686c00404](/phenotypic-features/edbac599-10a4-47e7-b223-454686c00404/).",
490                "level": 30,
491                "level_name": "INTERNAL_ACTION",
492                "name": "audit_item_status",
493                "path": "/human-donors/IGVFDO8547HLIG/"
494            },
495            {
496                "category": "mismatched status",
497                "detail": "Preview human donor [IGVFDO8547HLIG](/human-donors/IGVFDO8547HLIG/) has in progress subobject phenotypic feature [7ca1c142-3d4e-47fc-b5b8-0540d12993f8](/phenotypic-features/7ca1c142-3d4e-47fc-b5b8-0540d12993f8/).",
498                "level": 30,
499                "level_name": "INTERNAL_ACTION",
500                "name": "audit_item_status",
501                "path": "/human-donors/IGVFDO8547HLIG/"
502            }
503        ],
504        "NOT_COMPLIANT": [
505            {
506                "category": "missing sequence specification",
507                "detail": "Measurement set [IGVFDS3520MQEA](/measurement-sets/IGVFDS3520MQEA/) has sequence file(s): [IGVFFI1553LZUF](/sequence-files/IGVFFI1553LZUF/), [IGVFFI9509OFVK](/sequence-files/IGVFFI9509OFVK/), [IGVFFI9383PCKM](/sequence-files/IGVFFI9383PCKM/), [IGVFFI1647NAPT](/sequence-files/IGVFFI1647NAPT/) 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.",
508                "level": 50,
509                "level_name": "NOT_COMPLIANT",
510                "name": "audit_missing_seqspec",
511                "path": "/measurement-sets/IGVFDS3520MQEA/"
512            }
513        ],
514        "WARNING": [
515            {
516                "category": "missing analysis",
517                "detail": "Measurement set [IGVFDS3520MQEA](/measurement-sets/IGVFDS3520MQEA/) 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.",
518                "level": 40,
519                "level_name": "WARNING",
520                "name": "audit_input_for",
521                "path": "/measurement-sets/IGVFDS3520MQEA/"
522            }
523        ]
524    },
525    "award": {
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527        "component": "mapping",
528        "contact_pi": {
529            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
530            "title": "Ansuman Satpathy"
531        },
532        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
533    },
534    "control_for": [],
535    "controlled_access": false,
536    "creation_timestamp": "2025-03-19T19:44:46.255813+00:00",
537    "data_use_limitation_summaries": [
538        "No limitations"
539    ],
540    "donors": [
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542            "@id": "/human-donors/IGVFDO4103FHPT/",
543            "accession": "IGVFDO4103FHPT",
544            "aliases": [
545                "igvf:corces_donor_BANN9702"
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550        },
551        {
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554            "aliases": [
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556            ],
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558            "status": "preview",
559            "taxa": "Homo sapiens"
560        },
561        {
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563            "accession": "IGVFDO1997RFPJ",
564            "aliases": [
565                "igvf:corces_donor_BANN1340"
566            ],
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570        },
571        {
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576            ],
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580        },
581        {
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755    "lab": {
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757        "title": "Ryan Corces, Gladstone Institute UCSF"
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760    "onlist_files": [
761        "/tabular-files/IGVFFI7587TJLC/"
762    ],
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771            "accession": "IGVFDS1696QREL",
772            "status": "preview"
773        }
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778            "@type": [
779                "MultiplexedSample",
780                "Sample",
781                "Item"
782            ],
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784            "aliases": [
785                "igvf:corces_multiplexedSample_X036_G5"
786            ],
787            "classifications": [
788                "tissue",
789                "multiplexed sample"
790            ],
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793                    "@id": "/phenotype-terms/DOID_14330/",
794                    "status": "in progress",
795                    "term_name": "Parkinson's disease"
796                },
797                {
798                    "@id": "/phenotype-terms/DOID_9246/",
799                    "status": "in progress",
800                    "term_name": "cerebral amyloid angiopathy"
801                }
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808                    "status": "in progress"
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814                    "@id": "/sample-terms/UBERON_0001874/",
815                    "@type": [
816                        "SampleTerm",
817                        "OntologyTerm",
818                        "Item"
819                    ],
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821                    "summary": "putamen",
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824                {
825                    "@id": "/sample-terms/UBERON_0002038/",
826                    "@type": [
827                        "SampleTerm",
828                        "OntologyTerm",
829                        "Item"
830                    ],
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832                    "summary": "substantia nigra",
833                    "term_name": "substantia nigra"
834                },
835                {
836                    "@id": "/sample-terms/UBERON_0002129/",
837                    "@type": [
838                        "SampleTerm",
839                        "OntologyTerm",
840                        "Item"
841                    ],
842                    "status": "preview",
843                    "summary": "cerebellar cortex",
844                    "term_name": "cerebellar cortex"
845                },
846                {
847                    "@id": "/sample-terms/UBERON_0002740/",
848                    "@type": [
849                        "SampleTerm",
850                        "OntologyTerm",
851                        "Item"
852                    ],
853                    "status": "preview",
854                    "summary": "posterior cingulate gyrus",
855                    "term_name": "posterior cingulate gyrus"
856                },
857                {
858                    "@id": "/sample-terms/UBERON_0002771/",
859                    "@type": [
860                        "SampleTerm",
861                        "OntologyTerm",
862                        "Item"
863                    ],
864                    "status": "preview",
865                    "summary": "middle temporal gyrus",
866                    "term_name": "middle temporal gyrus"
867                }
868            ],
869            "status": "preview",
870            "summary": "multiplexed sample: Homo sapiens (female, 83 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 81 years) posterior cingulate gyrus tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 10 more samples",
871            "taxa": "Homo sapiens",
872            "treatments": []
873        }
874    ],
875    "schema_version": "26",
876    "status": "preview",
877    "submitted_by": {
878        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
879        "title": "Ryan Corces"
880    },
881    "submitted_files_timestamp": "2025-03-20T02:55:33.627201+00:00",
882    "summary": "single-nucleus ATAC-seq (10x multiome)",
883    "uuid": "fe1c0684-20ed-4a0a-a2f0-04d4340c8983"
884}