IGVFDS4249DVHL

1{
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3    "@id": "/measurement-sets/IGVFDS4249DVHL/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
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10    "aliases": [
11        "igvf:corces_measurementSet_RP010_G2_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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359            {
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383            {
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447            {
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463            {
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471            {
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495            {
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503            {
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505                "detail": "Preview human donor [IGVFDO9247BEUS](/human-donors/IGVFDO9247BEUS/) has in progress subobject phenotypic feature [59f6e0a8-5a94-41c3-a3ad-b1982138f286](/phenotypic-features/59f6e0a8-5a94-41c3-a3ad-b1982138f286/).",
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511            {
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513                "detail": "Preview human donor [IGVFDO9247BEUS](/human-donors/IGVFDO9247BEUS/) has in progress subobject phenotypic feature [e774cecf-7269-4269-a9c8-ef242ff0930a](/phenotypic-features/e774cecf-7269-4269-a9c8-ef242ff0930a/).",
514                "level": 30,
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519            {
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527            {
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529                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [95491ef2-b590-4c18-b81d-6c903ed626a4](/phenotypic-features/95491ef2-b590-4c18-b81d-6c903ed626a4/).",
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535            {
536                "category": "mismatched status",
537                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [c9ecdf8e-7c0f-473e-a8be-77797167794c](/phenotypic-features/c9ecdf8e-7c0f-473e-a8be-77797167794c/).",
538                "level": 30,
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543            {
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545                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [6a8d3945-6600-4f71-bc2d-3aa7cd079713](/phenotypic-features/6a8d3945-6600-4f71-bc2d-3aa7cd079713/).",
546                "level": 30,
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550            },
551            {
552                "category": "mismatched status",
553                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [29048a47-9d7d-4ad1-bc30-b97bd2c5e4d7](/phenotypic-features/29048a47-9d7d-4ad1-bc30-b97bd2c5e4d7/).",
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558            },
559            {
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561                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [793031fc-a40d-4951-9abf-09dcf84149cb](/phenotypic-features/793031fc-a40d-4951-9abf-09dcf84149cb/).",
562                "level": 30,
563                "level_name": "INTERNAL_ACTION",
564                "name": "audit_item_status",
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566            },
567            {
568                "category": "mismatched status",
569                "detail": "Preview human donor [IGVFDO7387JZDV](/human-donors/IGVFDO7387JZDV/) has in progress subobject phenotypic feature [721cdbe5-854d-428a-85b6-a444e6fe94c3](/phenotypic-features/721cdbe5-854d-428a-85b6-a444e6fe94c3/).",
570                "level": 30,
571                "level_name": "INTERNAL_ACTION",
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573                "path": "/human-donors/IGVFDO7387JZDV/"
574            },
575            {
576                "category": "mismatched status",
577                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [4f68640b-3f92-4906-9bac-808001031fbb](/phenotypic-features/4f68640b-3f92-4906-9bac-808001031fbb/).",
578                "level": 30,
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580                "name": "audit_item_status",
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582            },
583            {
584                "category": "mismatched status",
585                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [842c58cd-8b71-4cd6-a121-989c48f6a757](/phenotypic-features/842c58cd-8b71-4cd6-a121-989c48f6a757/).",
586                "level": 30,
587                "level_name": "INTERNAL_ACTION",
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590            },
591            {
592                "category": "mismatched status",
593                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [580639c7-8b7a-4e04-a362-38b90bb8ccef](/phenotypic-features/580639c7-8b7a-4e04-a362-38b90bb8ccef/).",
594                "level": 30,
595                "level_name": "INTERNAL_ACTION",
596                "name": "audit_item_status",
597                "path": "/human-donors/IGVFDO5912PIZP/"
598            },
599            {
600                "category": "mismatched status",
601                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [b59c47e4-8549-4b63-95c7-c7b732cd80a1](/phenotypic-features/b59c47e4-8549-4b63-95c7-c7b732cd80a1/).",
602                "level": 30,
603                "level_name": "INTERNAL_ACTION",
604                "name": "audit_item_status",
605                "path": "/human-donors/IGVFDO5912PIZP/"
606            },
607            {
608                "category": "mismatched status",
609                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [b4968851-2538-49ab-a27e-be55b86b05b9](/phenotypic-features/b4968851-2538-49ab-a27e-be55b86b05b9/).",
610                "level": 30,
611                "level_name": "INTERNAL_ACTION",
612                "name": "audit_item_status",
613                "path": "/human-donors/IGVFDO5912PIZP/"
614            },
615            {
616                "category": "mismatched status",
617                "detail": "Preview human donor [IGVFDO5912PIZP](/human-donors/IGVFDO5912PIZP/) has in progress subobject phenotypic feature [58a6b3f4-d283-4561-a436-8c6d81773bea](/phenotypic-features/58a6b3f4-d283-4561-a436-8c6d81773bea/).",
618                "level": 30,
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622            }
623        ],
624        "NOT_COMPLIANT": [
625            {
626                "category": "missing sequence specification",
627                "detail": "Measurement set [IGVFDS4249DVHL](/measurement-sets/IGVFDS4249DVHL/) has sequence file(s): [IGVFFI4265GPMZ](/sequence-files/IGVFFI4265GPMZ/), [IGVFFI4618CJZP](/sequence-files/IGVFFI4618CJZP/), [IGVFFI8974KXCG](/sequence-files/IGVFFI8974KXCG/), [IGVFFI3266UTHS](/sequence-files/IGVFFI3266UTHS/), [IGVFFI9897FYEM](/sequence-files/IGVFFI9897FYEM/), [IGVFFI4522BKOI](/sequence-files/IGVFFI4522BKOI/), [IGVFFI3847NVKF](/sequence-files/IGVFFI3847NVKF/), [IGVFFI0148QZVW](/sequence-files/IGVFFI0148QZVW/), [IGVFFI0798RGHR](/sequence-files/IGVFFI0798RGHR/), [IGVFFI0776JKUE](/sequence-files/IGVFFI0776JKUE/), [IGVFFI0125IBBM](/sequence-files/IGVFFI0125IBBM/), [IGVFFI1214SFFA](/sequence-files/IGVFFI1214SFFA/), [IGVFFI1401IKHX](/sequence-files/IGVFFI1401IKHX/), [IGVFFI0393AEZF](/sequence-files/IGVFFI0393AEZF/), [IGVFFI4384KHIR](/sequence-files/IGVFFI4384KHIR/), [IGVFFI9460EPWN](/sequence-files/IGVFFI9460EPWN/) 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.",
628                "level": 50,
629                "level_name": "NOT_COMPLIANT",
630                "name": "audit_missing_seqspec",
631                "path": "/measurement-sets/IGVFDS4249DVHL/"
632            },
633            {
634                "category": "missing strand specificity",
635                "detail": "Measurement set [IGVFDS4249DVHL](/measurement-sets/IGVFDS4249DVHL/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
636                "level": 50,
637                "level_name": "NOT_COMPLIANT",
638                "name": "audit_missing_strand_specificity",
639                "path": "/measurement-sets/IGVFDS4249DVHL/"
640            }
641        ],
642        "WARNING": [
643            {
644                "category": "missing analysis",
645                "detail": "Measurement set [IGVFDS4249DVHL](/measurement-sets/IGVFDS4249DVHL/) 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.",
646                "level": 40,
647                "level_name": "WARNING",
648                "name": "audit_input_for",
649                "path": "/measurement-sets/IGVFDS4249DVHL/"
650            }
651        ]
652    },
653    "award": {
654        "@id": "/awards/HG012076/",
655        "component": "mapping",
656        "contact_pi": {
657            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
658            "title": "Ansuman Satpathy"
659        },
660        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
661    },
662    "control_for": [],
663    "controlled_access": false,
664    "creation_timestamp": "2025-03-19T19:53:17.741787+00:00",
665    "data_use_limitation_summaries": [
666        "No limitations"
667    ],
668    "donors": [
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671            "accession": "IGVFDO6013FYCW",
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674            ],
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678        },
679        {
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681            "accession": "IGVFDO7095OCLJ",
682            "aliases": [
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684            ],
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688        },
689        {
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691            "accession": "IGVFDO1464XWYC",
692            "aliases": [
693                "igvf:corces_donor_BANN1809"
694            ],
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698        },
699        {
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701            "accession": "IGVFDO9247BEUS",
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709        {
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719        {
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728        },
729        {
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1183            "accession": "IGVFDS9748IKAS",
1184            "status": "preview"
1185        }
1186    ],
1187    "samples": [
1188        {
1189            "@id": "/multiplexed-samples/IGVFSM8981GXZB/",
1190            "@type": [
1191                "MultiplexedSample",
1192                "Sample",
1193                "Item"
1194            ],
1195            "accession": "IGVFSM8981GXZB",
1196            "aliases": [
1197                "igvf:corces_multiplexedSample_RP010_G2"
1198            ],
1199            "classifications": [
1200                "tissue",
1201                "multiplexed sample"
1202            ],
1203            "disease_terms": [
1204                {
1205                    "@id": "/phenotype-terms/DOID_0080832/",
1206                    "status": "in progress",
1207                    "term_name": "mild cognitive impairment"
1208                },
1209                {
1210                    "@id": "/phenotype-terms/DOID_14330/",
1211                    "status": "in progress",
1212                    "term_name": "Parkinson's disease"
1213                },
1214                {
1215                    "@id": "/phenotype-terms/DOID_9246/",
1216                    "status": "in progress",
1217                    "term_name": "cerebral amyloid angiopathy"
1218                }
1219            ],
1220            "institutional_certificates": [
1221                {
1222                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
1223                    "certificate_identifier": "IP115-05",
1224                    "controlled_access": false,
1225                    "status": "in progress"
1226                }
1227            ],
1228            "modifications": [],
1229            "sample_terms": [
1230                {
1231                    "@id": "/sample-terms/UBERON_0001874/",
1232                    "@type": [
1233                        "SampleTerm",
1234                        "OntologyTerm",
1235                        "Item"
1236                    ],
1237                    "status": "preview",
1238                    "summary": "putamen",
1239                    "term_name": "putamen"
1240                },
1241                {
1242                    "@id": "/sample-terms/UBERON_0002038/",
1243                    "@type": [
1244                        "SampleTerm",
1245                        "OntologyTerm",
1246                        "Item"
1247                    ],
1248                    "status": "preview",
1249                    "summary": "substantia nigra",
1250                    "term_name": "substantia nigra"
1251                },
1252                {
1253                    "@id": "/sample-terms/UBERON_0002129/",
1254                    "@type": [
1255                        "SampleTerm",
1256                        "OntologyTerm",
1257                        "Item"
1258                    ],
1259                    "status": "preview",
1260                    "summary": "cerebellar cortex",
1261                    "term_name": "cerebellar cortex"
1262                },
1263                {
1264                    "@id": "/sample-terms/UBERON_0002740/",
1265                    "@type": [
1266                        "SampleTerm",
1267                        "OntologyTerm",
1268                        "Item"
1269                    ],
1270                    "status": "preview",
1271                    "summary": "posterior cingulate gyrus",
1272                    "term_name": "posterior cingulate gyrus"
1273                },
1274                {
1275                    "@id": "/sample-terms/UBERON_0002771/",
1276                    "@type": [
1277                        "SampleTerm",
1278                        "OntologyTerm",
1279                        "Item"
1280                    ],
1281                    "status": "preview",
1282                    "summary": "middle temporal gyrus",
1283                    "term_name": "middle temporal gyrus"
1284                }
1285            ],
1286            "status": "preview",
1287            "summary": "multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 78 years) putamen tissue associated with Parkinson's disease, mild cognitive impairment; ... and 12 more samples",
1288            "taxa": "Homo sapiens",
1289            "treatments": []
1290        }
1291    ],
1292    "schema_version": "26",
1293    "status": "preview",
1294    "submitted_by": {
1295        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1296        "title": "Ryan Corces"
1297    },
1298    "submitted_files_timestamp": "2025-03-20T16:42:25.593983+00:00",
1299    "summary": "single-nucleus ATAC-seq (10x multiome)",
1300    "uuid": "4001feef-3bb3-4488-adc3-4fe03d7e8277"
1301}