IGVFDS7473ITUN

1{
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4    "@type": [
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10    "aliases": [
11        "igvf:corces_measurementSet_RP013_G2_RNA"
12    ],
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14        "@id": "/assay-terms/OBI_0003109/",
15        "assay_slims": [
16            "gene expression"
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18        "status": "released",
19        "term_name": "single-nucleus RNA sequencing assay"
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 [IGVFDS7473ITUN](/measurement-sets/IGVFDS7473ITUN/) has sequence file(s): [IGVFFI7174DBGB](/sequence-files/IGVFFI7174DBGB/), [IGVFFI4340HEBF](/sequence-files/IGVFFI4340HEBF/), [IGVFFI6240EWMD](/sequence-files/IGVFFI6240EWMD/), [IGVFFI5736FCYQ](/sequence-files/IGVFFI5736FCYQ/), [IGVFFI5995JAKP](/sequence-files/IGVFFI5995JAKP/), [IGVFFI6957EPMY](/sequence-files/IGVFFI6957EPMY/), [IGVFFI9907ZHVC](/sequence-files/IGVFFI9907ZHVC/), [IGVFFI6904FRJC](/sequence-files/IGVFFI6904FRJC/), [IGVFFI5972ZIPU](/sequence-files/IGVFFI5972ZIPU/), [IGVFFI5018CBYB](/sequence-files/IGVFFI5018CBYB/), [IGVFFI6294UCRX](/sequence-files/IGVFFI6294UCRX/), [IGVFFI8047SGLA](/sequence-files/IGVFFI8047SGLA/), [IGVFFI7565MRXN](/sequence-files/IGVFFI7565MRXN/), [IGVFFI1319YXOG](/sequence-files/IGVFFI1319YXOG/), [IGVFFI6498QEEG](/sequence-files/IGVFFI6498QEEG/), [IGVFFI6151IZOF](/sequence-files/IGVFFI6151IZOF/) 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/IGVFDS7473ITUN/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS7473ITUN](/measurement-sets/IGVFDS7473ITUN/) 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/IGVFDS7473ITUN/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS7473ITUN](/measurement-sets/IGVFDS7473ITUN/) 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/IGVFDS7473ITUN/"
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": "2025-03-19T21:42:48.335278+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": [
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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        {
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815            "accession": "IGVFDO0180JQCL",
816            "aliases": [
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818            ],
819            "sex": "female",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
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825            "accession": "IGVFDO8155MCUV",
826            "aliases": [
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828            ],
829            "sex": "female",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
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835            "accession": "IGVFDO7606UOXI",
836            "aliases": [
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838            ],
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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        {
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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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866            "aliases": [
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868            ],
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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        {
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885            "accession": "IGVFDO4053HEKW",
886            "aliases": [
887                "igvf:corces_donor_BANN1317"
888            ],
889            "sex": "male",
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891            "taxa": "Homo sapiens"
892        },
893        {
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895            "accession": "IGVFDO1797DNPW",
896            "aliases": [
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898            ],
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900            "status": "preview",
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902        },
903        {
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906            "aliases": [
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908            ],
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910            "status": "preview",
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912        },
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918            ],
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920            "status": "preview",
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930            "status": "preview",
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980        },
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987            "content_type": "reads",
988            "controlled_access": false,
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994            "sequencing_platform": {
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996                "status": "released",
997                "term_name": "Illumina NovaSeq X"
998            },
999            "status": "preview",
1000            "submitted_file_name": "Multiome_RNA_RP013_G2_L002_P062_S22_L005_R1_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
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1005            "accession": "IGVFFI5736FCYQ",
1006            "aliases": [
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1009            "content_type": "reads",
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1024        },
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1027            "accession": "IGVFFI5995JAKP",
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1046        },
1047        {
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1050            "aliases": [
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1082            "sequencing_platform": {
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1085                "term_name": "Illumina NovaSeq X"
1086            },
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1088            "submitted_file_name": "Multiome_RNA_RP013_G2_L002_P062_S22_L007_I2_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
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1093            "accession": "IGVFFI6904FRJC",
1094            "aliases": [
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1096            ],
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1099            "creation_timestamp": "2025-03-20T21:02:46.019340+00:00",
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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_RNA_RP013_G2_L002_P062_S22_L005_I2_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI5972ZIPU/",
1115            "accession": "IGVFFI5972ZIPU",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_RNA_RP013_G2_P062_L006_R2"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T21:03:08.372692+00:00",
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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_RNA_RP013_G2_L002_P062_S22_L006_R2_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI5018CBYB/",
1137            "accession": "IGVFFI5018CBYB",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_RNA_RP013_G2_P062_L005_I1"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T21:02:43.116826+00:00",
1144            "file_format": "fastq",
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1148            "sequencing_platform": {
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1150                "status": "released",
1151                "term_name": "Illumina NovaSeq X"
1152            },
1153            "status": "preview",
1154            "submitted_file_name": "Multiome_RNA_RP013_G2_L002_P062_S22_L005_I1_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI6294UCRX/",
1159            "accession": "IGVFFI6294UCRX",
1160            "aliases": [
1161                "igvf:corces_sequenceFile_RNA_RP013_G2_P062_L006_I1"
1162            ],
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1293        "title": "Ryan Corces, Gladstone Institute UCSF"
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1296    "onlist_files": [
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1298    ],
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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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1309        }
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1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
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1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP013_G2"
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1324                "tissue",
1325                "multiplexed sample"
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1327            "disease_terms": [
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1330                    "status": "in progress",
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1332                },
1333                {
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1337                },
1338                {
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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                {
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1350                    "status": "released",
1351                    "term_name": "Alzheimer disease"
1352                }
1353            ],
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1366                    "@type": [
1367                        "SampleTerm",
1368                        "OntologyTerm",
1369                        "Item"
1370                    ],
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1374                },
1375                {
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1377                    "@type": [
1378                        "SampleTerm",
1379                        "OntologyTerm",
1380                        "Item"
1381                    ],
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1384                    "term_name": "substantia nigra"
1385                },
1386                {
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1388                    "@type": [
1389                        "SampleTerm",
1390                        "OntologyTerm",
1391                        "Item"
1392                    ],
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1396                },
1397                {
1398                    "@id": "/sample-terms/UBERON_0002771/",
1399                    "@type": [
1400                        "SampleTerm",
1401                        "OntologyTerm",
1402                        "Item"
1403                    ],
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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        }
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1419        "title": "Ryan Corces"
1420    },
1421    "submitted_files_timestamp": "2025-03-20T21:02:43.116826+00:00",
1422    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
1423    "uuid": "3bda4ae5-fe70-4ca7-9ab3-e49b3f2bd293"
1424}