IGVFDS2373GWYA

1{
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4    "@type": [
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9    "accession": "IGVFDS2373GWYA",
10    "aliases": [
11        "igvf:corces_measurementSet_RP013_G1_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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705                "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/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO3971UIZC/"
710            },
711            {
712                "category": "mismatched status",
713                "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/).",
714                "level": 30,
715                "level_name": "INTERNAL_ACTION",
716                "name": "audit_item_status",
717                "path": "/human-donors/IGVFDO3971UIZC/"
718            },
719            {
720                "category": "mismatched status",
721                "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/).",
722                "level": 30,
723                "level_name": "INTERNAL_ACTION",
724                "name": "audit_item_status",
725                "path": "/human-donors/IGVFDO3971UIZC/"
726            }
727        ],
728        "NOT_COMPLIANT": [
729            {
730                "category": "missing sequence specification",
731                "detail": "Measurement set [IGVFDS2373GWYA](/measurement-sets/IGVFDS2373GWYA/) has sequence file(s): [IGVFFI2184MBGW](/sequence-files/IGVFFI2184MBGW/), [IGVFFI8464IWZJ](/sequence-files/IGVFFI8464IWZJ/), [IGVFFI0495TNKF](/sequence-files/IGVFFI0495TNKF/), [IGVFFI7075PLQB](/sequence-files/IGVFFI7075PLQB/), [IGVFFI6227NVBN](/sequence-files/IGVFFI6227NVBN/), [IGVFFI7419HBZV](/sequence-files/IGVFFI7419HBZV/), [IGVFFI3364JMMG](/sequence-files/IGVFFI3364JMMG/), [IGVFFI7976SXMO](/sequence-files/IGVFFI7976SXMO/), [IGVFFI9296UCVF](/sequence-files/IGVFFI9296UCVF/), [IGVFFI5453OPXB](/sequence-files/IGVFFI5453OPXB/), [IGVFFI2616AROV](/sequence-files/IGVFFI2616AROV/), [IGVFFI7879IDDS](/sequence-files/IGVFFI7879IDDS/), [IGVFFI5614IDYR](/sequence-files/IGVFFI5614IDYR/), [IGVFFI9375DMUJ](/sequence-files/IGVFFI9375DMUJ/), [IGVFFI2776RKQQ](/sequence-files/IGVFFI2776RKQQ/), [IGVFFI6949VCFS](/sequence-files/IGVFFI6949VCFS/) 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.",
732                "level": 50,
733                "level_name": "NOT_COMPLIANT",
734                "name": "audit_missing_seqspec",
735                "path": "/measurement-sets/IGVFDS2373GWYA/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS2373GWYA](/measurement-sets/IGVFDS2373GWYA/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
740                "level": 50,
741                "level_name": "NOT_COMPLIANT",
742                "name": "audit_missing_strand_specificity",
743                "path": "/measurement-sets/IGVFDS2373GWYA/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS2373GWYA](/measurement-sets/IGVFDS2373GWYA/) 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.",
750                "level": 40,
751                "level_name": "WARNING",
752                "name": "audit_input_for",
753                "path": "/measurement-sets/IGVFDS2373GWYA/"
754            }
755        ]
756    },
757    "award": {
758        "@id": "/awards/HG012076/",
759        "component": "mapping",
760        "contact_pi": {
761            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
762            "title": "Ansuman Satpathy"
763        },
764        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
765    },
766    "control_for": [],
767    "controlled_access": false,
768    "creation_timestamp": "2025-03-19T19:54:15.704961+00:00",
769    "data_use_limitation_summaries": [
770        "No limitations"
771    ],
772    "donors": [
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774            "@id": "/human-donors/IGVFDO4108VCBA/",
775            "accession": "IGVFDO4108VCBA",
776            "aliases": [
777                "igvf:corces_donor_BANN0325"
778            ],
779            "sex": "male",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
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785            "accession": "IGVFDO7754VJKM",
786            "aliases": [
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788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO4170HAEN/",
795            "accession": "IGVFDO4170HAEN",
796            "aliases": [
797                "igvf:corces_donor_BANN1864"
798            ],
799            "sex": "male",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
804            "@id": "/human-donors/IGVFDO8344LUQZ/",
805            "accession": "IGVFDO8344LUQZ",
806            "aliases": [
807                "igvf:corces_donor_BANN0621"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
814            "@id": "/human-donors/IGVFDO0180JQCL/",
815            "accession": "IGVFDO0180JQCL",
816            "aliases": [
817                "igvf:corces_donor_BANN1344"
818            ],
819            "sex": "female",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
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825            "accession": "IGVFDO8155MCUV",
826            "aliases": [
827                "igvf:corces_donor_BANN0437"
828            ],
829            "sex": "female",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
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835            "accession": "IGVFDO7606UOXI",
836            "aliases": [
837                "igvf:corces_donor_BANN1570"
838            ],
839            "sex": "male",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
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845            "accession": "IGVFDO8670MHXE",
846            "aliases": [
847                "igvf:corces_donor_BANN0874"
848            ],
849            "sex": "female",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO0698ZMAQ/",
855            "accession": "IGVFDO0698ZMAQ",
856            "aliases": [
857                "igvf:corces_donor_BANN1569"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
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865            "accession": "IGVFDO3971UIZC",
866            "aliases": [
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868            ],
869            "sex": "female",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
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875            "accession": "IGVFDO8800RKVB",
876            "aliases": [
877                "igvf:corces_donor_BANN1872"
878            ],
879            "sex": "female",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO4053HEKW/",
885            "accession": "IGVFDO4053HEKW",
886            "aliases": [
887                "igvf:corces_donor_BANN1317"
888            ],
889            "sex": "male",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        },
893        {
894            "@id": "/human-donors/IGVFDO1797DNPW/",
895            "accession": "IGVFDO1797DNPW",
896            "aliases": [
897                "igvf:corces_donor_BANN1827"
898            ],
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900            "status": "preview",
901            "taxa": "Homo sapiens"
902        },
903        {
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905            "accession": "IGVFDO4273OHGB",
906            "aliases": [
907                "igvf:corces_donor_BANN0322"
908            ],
909            "sex": "female",
910            "status": "preview",
911            "taxa": "Homo sapiens"
912        },
913        {
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915            "accession": "IGVFDO7315DYIP",
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918            ],
919            "sex": "female",
920            "status": "preview",
921            "taxa": "Homo sapiens"
922        },
923        {
924            "@id": "/human-donors/IGVFDO5205IAEO/",
925            "accession": "IGVFDO5205IAEO",
926            "aliases": [
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930            "status": "preview",
931            "taxa": "Homo sapiens"
932        }
933    ],
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940            "aliases": [
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950            "sequencing_platform": {
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954            },
955            "status": "preview",
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957            "upload_status": "validated"
958        },
959        {
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963                "igvf:corces_sequenceFile_ATAC_RP013_G1_P061_L002_R2"
964            ],
965            "content_type": "reads",
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967            "creation_timestamp": "2025-03-20T20:20:14.252705+00:00",
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978            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L002_R2_001.fastq.gz",
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980        },
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984            "aliases": [
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987            "content_type": "reads",
988            "controlled_access": false,
989            "creation_timestamp": "2025-03-20T20:20:17.559313+00:00",
990            "file_format": "fastq",
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994            "sequencing_platform": {
995                "@id": "/platform-terms/EFO_0022840/",
996                "status": "released",
997                "term_name": "Illumina NovaSeq X"
998            },
999            "status": "preview",
1000            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L002_R3_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
1004            "@id": "/sequence-files/IGVFFI7075PLQB/",
1005            "accession": "IGVFFI7075PLQB",
1006            "aliases": [
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1008            ],
1009            "content_type": "reads",
1010            "controlled_access": false,
1011            "creation_timestamp": "2025-03-20T20:20:07.218396+00:00",
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1019                "term_name": "Illumina NovaSeq X"
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1021            "status": "preview",
1022            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L002_I1_001.fastq.gz",
1023            "upload_status": "validated"
1024        },
1025        {
1026            "@id": "/sequence-files/IGVFFI6227NVBN/",
1027            "accession": "IGVFFI6227NVBN",
1028            "aliases": [
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1031            "content_type": "reads",
1032            "controlled_access": false,
1033            "creation_timestamp": "2025-03-20T20:20:10.789797+00:00",
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1038            "sequencing_platform": {
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1040                "status": "released",
1041                "term_name": "Illumina NovaSeq X"
1042            },
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1044            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L002_R1_001.fastq.gz",
1045            "upload_status": "validated"
1046        },
1047        {
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1049            "accession": "IGVFFI7419HBZV",
1050            "aliases": [
1051                "igvf:corces_sequenceFile_ATAC_RP013_G1_P061_L003_R3"
1052            ],
1053            "content_type": "reads",
1054            "controlled_access": false,
1055            "creation_timestamp": "2025-03-20T20:20:31.738337+00:00",
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1060            "sequencing_platform": {
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1063                "term_name": "Illumina NovaSeq X"
1064            },
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1067            "upload_status": "validated"
1068        },
1069        {
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1071            "accession": "IGVFFI3364JMMG",
1072            "aliases": [
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1074            ],
1075            "content_type": "reads",
1076            "controlled_access": false,
1077            "creation_timestamp": "2025-03-20T20:20:43.712860+00:00",
1078            "file_format": "fastq",
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1082            "sequencing_platform": {
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1084                "status": "released",
1085                "term_name": "Illumina NovaSeq X"
1086            },
1087            "status": "preview",
1088            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L004_R2_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
1092            "@id": "/sequence-files/IGVFFI7976SXMO/",
1093            "accession": "IGVFFI7976SXMO",
1094            "aliases": [
1095                "igvf:corces_sequenceFile_ATAC_RP013_G1_P061_L003_R2"
1096            ],
1097            "content_type": "reads",
1098            "controlled_access": false,
1099            "creation_timestamp": "2025-03-20T20:20:28.144528+00:00",
1100            "file_format": "fastq",
1101            "file_size": 1058899183,
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1103            "s3_uri": "s3://igvf-files/2025/03/20/dd105a5e-e436-4a3b-9af0-0d817bb80125/IGVFFI7976SXMO.fastq.gz",
1104            "sequencing_platform": {
1105                "@id": "/platform-terms/EFO_0022840/",
1106                "status": "released",
1107                "term_name": "Illumina NovaSeq X"
1108            },
1109            "status": "preview",
1110            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L003_R2_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI9296UCVF/",
1115            "accession": "IGVFFI9296UCVF",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_ATAC_RP013_G1_P061_L001_R1"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T20:19:55.639794+00:00",
1122            "file_format": "fastq",
1123            "file_size": 1890005825,
1124            "href": "/sequence-files/IGVFFI9296UCVF/@@download/IGVFFI9296UCVF.fastq.gz",
1125            "s3_uri": "s3://igvf-files/2025/03/20/7ef6b09a-9912-4ab7-94e4-8b51d2b00d70/IGVFFI9296UCVF.fastq.gz",
1126            "sequencing_platform": {
1127                "@id": "/platform-terms/EFO_0022840/",
1128                "status": "released",
1129                "term_name": "Illumina NovaSeq X"
1130            },
1131            "status": "preview",
1132            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L001_R1_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI5453OPXB/",
1137            "accession": "IGVFFI5453OPXB",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_ATAC_RP013_G1_P061_L003_I1"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T20:20:21.076331+00:00",
1144            "file_format": "fastq",
1145            "file_size": 464224122,
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1147            "s3_uri": "s3://igvf-files/2025/03/20/2c8365d2-4780-4d2c-b8fc-bf2021460afd/IGVFFI5453OPXB.fastq.gz",
1148            "sequencing_platform": {
1149                "@id": "/platform-terms/EFO_0022840/",
1150                "status": "released",
1151                "term_name": "Illumina NovaSeq X"
1152            },
1153            "status": "preview",
1154            "submitted_file_name": "Multiome_ATAC_RP013_G1_L001_P061_S1_L003_I1_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI2616AROV/",
1159            "accession": "IGVFFI2616AROV",
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1269            "accession": "IGVFFI6949VCFS",
1270            "aliases": [
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1293        "title": "Ryan Corces, Gladstone Institute UCSF"
1294    },
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1296    "onlist_files": [
1297        "/tabular-files/IGVFFI7587TJLC/"
1298    ],
1299    "onlist_method": "no combination",
1300    "preferred_assay_title": "10x multiome",
1301    "protocols": [
1302        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1303    ],
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1307            "accession": "IGVFDS8759JYNP",
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1309        }
1310    ],
1311    "samples": [
1312        {
1313            "@id": "/multiplexed-samples/IGVFSM3819ZCMN/",
1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
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1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP013_G1"
1322            ],
1323            "classifications": [
1324                "tissue",
1325                "multiplexed sample"
1326            ],
1327            "disease_terms": [
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1330                    "status": "in progress",
1331                    "term_name": "mild cognitive impairment"
1332                },
1333                {
1334                    "@id": "/phenotype-terms/DOID_14330/",
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1336                    "term_name": "Parkinson's disease"
1337                },
1338                {
1339                    "@id": "/phenotype-terms/DOID_2377/",
1340                    "status": "in progress",
1341                    "term_name": "multiple sclerosis"
1342                },
1343                {
1344                    "@id": "/phenotype-terms/DOID_9246/",
1345                    "status": "in progress",
1346                    "term_name": "cerebral amyloid angiopathy"
1347                },
1348                {
1349                    "@id": "/phenotype-terms/MONDO_0004975/",
1350                    "status": "released",
1351                    "term_name": "Alzheimer disease"
1352                }
1353            ],
1354            "institutional_certificates": [
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1357                    "certificate_identifier": "IP115-05",
1358                    "controlled_access": false,
1359                    "status": "in progress"
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1363            "sample_terms": [
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1366                    "@type": [
1367                        "SampleTerm",
1368                        "OntologyTerm",
1369                        "Item"
1370                    ],
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1374                },
1375                {
1376                    "@id": "/sample-terms/UBERON_0002038/",
1377                    "@type": [
1378                        "SampleTerm",
1379                        "OntologyTerm",
1380                        "Item"
1381                    ],
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1383                    "summary": "substantia nigra",
1384                    "term_name": "substantia nigra"
1385                },
1386                {
1387                    "@id": "/sample-terms/UBERON_0002740/",
1388                    "@type": [
1389                        "SampleTerm",
1390                        "OntologyTerm",
1391                        "Item"
1392                    ],
1393                    "status": "preview",
1394                    "summary": "posterior cingulate gyrus",
1395                    "term_name": "posterior cingulate gyrus"
1396                },
1397                {
1398                    "@id": "/sample-terms/UBERON_0002771/",
1399                    "@type": [
1400                        "SampleTerm",
1401                        "OntologyTerm",
1402                        "Item"
1403                    ],
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1405                    "summary": "middle temporal gyrus",
1406                    "term_name": "middle temporal gyrus"
1407                }
1408            ],
1409            "status": "preview",
1410            "summary": "multiplexed sample: Homo sapiens (female, 86 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 78 years) posterior cingulate gyrus tissue associated with Parkinson's disease; ... and 14 more samples",
1411            "taxa": "Homo sapiens",
1412            "treatments": []
1413        }
1414    ],
1415    "schema_version": "26",
1416    "status": "preview",
1417    "submitted_by": {
1418        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1419        "title": "Ryan Corces"
1420    },
1421    "submitted_files_timestamp": "2025-03-20T20:19:51.788127+00:00",
1422    "summary": "single-nucleus ATAC-seq (10x multiome)",
1423    "uuid": "266c39cb-6682-4ac9-828e-3e0f2614cef7"
1424}