IGVFDS4413FCPJ

1{
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10    "aliases": [
11        "igvf:corces_measurementSet_RP013_G3_RNA"
12    ],
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15        "assay_slims": [
16            "gene expression"
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18        "status": "released",
19        "term_name": "single-nucleus RNA sequencing assay"
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703            {
704                "category": "mismatched status",
705                "detail": "Preview human donor [IGVFDO5205IAEO](/human-donors/IGVFDO5205IAEO/) has in progress subobject phenotypic feature [5d86271f-e200-458e-b626-d45775c1f778](/phenotypic-features/5d86271f-e200-458e-b626-d45775c1f778/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO5205IAEO/"
710            },
711            {
712                "category": "mismatched status",
713                "detail": "Preview human donor [IGVFDO5205IAEO](/human-donors/IGVFDO5205IAEO/) has in progress subobject phenotypic feature [f57b6265-94b7-4979-be4c-73ef23b5faba](/phenotypic-features/f57b6265-94b7-4979-be4c-73ef23b5faba/).",
714                "level": 30,
715                "level_name": "INTERNAL_ACTION",
716                "name": "audit_item_status",
717                "path": "/human-donors/IGVFDO5205IAEO/"
718            },
719            {
720                "category": "mismatched status",
721                "detail": "Preview human donor [IGVFDO5205IAEO](/human-donors/IGVFDO5205IAEO/) has in progress subobject phenotypic feature [87d488ba-ef89-494c-8024-bee2b8535732](/phenotypic-features/87d488ba-ef89-494c-8024-bee2b8535732/).",
722                "level": 30,
723                "level_name": "INTERNAL_ACTION",
724                "name": "audit_item_status",
725                "path": "/human-donors/IGVFDO5205IAEO/"
726            }
727        ],
728        "NOT_COMPLIANT": [
729            {
730                "category": "missing sequence specification",
731                "detail": "Measurement set [IGVFDS4413FCPJ](/measurement-sets/IGVFDS4413FCPJ/) has sequence file(s): [IGVFFI8198HMNG](/sequence-files/IGVFFI8198HMNG/), [IGVFFI5979EIZI](/sequence-files/IGVFFI5979EIZI/), [IGVFFI3063IFRJ](/sequence-files/IGVFFI3063IFRJ/), [IGVFFI7520RNNR](/sequence-files/IGVFFI7520RNNR/), [IGVFFI3513VXZQ](/sequence-files/IGVFFI3513VXZQ/), [IGVFFI3735TQAL](/sequence-files/IGVFFI3735TQAL/), [IGVFFI6574KUBC](/sequence-files/IGVFFI6574KUBC/), [IGVFFI3623MMKK](/sequence-files/IGVFFI3623MMKK/), [IGVFFI3416PWFS](/sequence-files/IGVFFI3416PWFS/), [IGVFFI2308TXQD](/sequence-files/IGVFFI2308TXQD/), [IGVFFI4049CZMX](/sequence-files/IGVFFI4049CZMX/), [IGVFFI0112WNSP](/sequence-files/IGVFFI0112WNSP/), [IGVFFI8565SFYW](/sequence-files/IGVFFI8565SFYW/), [IGVFFI3765QRAX](/sequence-files/IGVFFI3765QRAX/), [IGVFFI9784UOMW](/sequence-files/IGVFFI9784UOMW/), [IGVFFI4076OJRC](/sequence-files/IGVFFI4076OJRC/) 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/IGVFDS4413FCPJ/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS4413FCPJ](/measurement-sets/IGVFDS4413FCPJ/) 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/IGVFDS4413FCPJ/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS4413FCPJ](/measurement-sets/IGVFDS4413FCPJ/) 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/IGVFDS4413FCPJ/"
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": "2025-03-19T21:42:50.096470+00:00",
769    "data_use_limitation_summaries": [
770        "No limitations"
771    ],
772    "donors": [
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774            "@id": "/human-donors/IGVFDO0698ZMAQ/",
775            "accession": "IGVFDO0698ZMAQ",
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": "IGVFDO4170HAEN",
786            "aliases": [
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788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO8670MHXE/",
795            "accession": "IGVFDO8670MHXE",
796            "aliases": [
797                "igvf:corces_donor_BANN0874"
798            ],
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800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
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805            "accession": "IGVFDO4108VCBA",
806            "aliases": [
807                "igvf:corces_donor_BANN0325"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
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815            "accession": "IGVFDO1797DNPW",
816            "aliases": [
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818            ],
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820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
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825            "accession": "IGVFDO7315DYIP",
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": "IGVFDO3971UIZC",
836            "aliases": [
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838            ],
839            "sex": "female",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
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845            "accession": "IGVFDO0180JQCL",
846            "aliases": [
847                "igvf:corces_donor_BANN1344"
848            ],
849            "sex": "female",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
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855            "accession": "IGVFDO7606UOXI",
856            "aliases": [
857                "igvf:corces_donor_BANN1570"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
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865            "accession": "IGVFDO8155MCUV",
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": "IGVFDO7754VJKM",
876            "aliases": [
877                "igvf:corces_donor_BANN0341"
878            ],
879            "sex": "male",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
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885            "accession": "IGVFDO8800RKVB",
886            "aliases": [
887                "igvf:corces_donor_BANN1872"
888            ],
889            "sex": "female",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        },
893        {
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895            "accession": "IGVFDO8344LUQZ",
896            "aliases": [
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898            ],
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900            "status": "preview",
901            "taxa": "Homo sapiens"
902        },
903        {
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906            "aliases": [
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908            ],
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910            "status": "preview",
911            "taxa": "Homo sapiens"
912        },
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918            ],
919            "sex": "male",
920            "status": "preview",
921            "taxa": "Homo sapiens"
922        },
923        {
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930            "status": "preview",
931            "taxa": "Homo sapiens"
932        }
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953                "term_name": "Illumina NovaSeq X"
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958        },
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978            "submitted_file_name": "Multiome_RNA_RP013_G3_L003_P062_S23_L008_I2_001.fastq.gz",
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984            "aliases": [
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986            ],
987            "content_type": "reads",
988            "controlled_access": false,
989            "creation_timestamp": "2025-03-20T21:03:55.198325+00:00",
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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_RNA_RP013_G3_L003_P062_S23_L005_R2_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
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1005            "accession": "IGVFFI7520RNNR",
1006            "aliases": [
1007                "igvf:corces_sequenceFile_RNA_RP013_G3_P062_L005_I1"
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1009            "content_type": "reads",
1010            "controlled_access": false,
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1016            "sequencing_platform": {
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1019                "term_name": "Illumina NovaSeq X"
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1021            "status": "preview",
1022            "submitted_file_name": "Multiome_RNA_RP013_G3_L003_P062_S23_L005_I1_001.fastq.gz",
1023            "upload_status": "validated"
1024        },
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1027            "accession": "IGVFFI3513VXZQ",
1028            "aliases": [
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1041                "term_name": "Illumina NovaSeq X"
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1044            "submitted_file_name": "Multiome_RNA_RP013_G3_L003_P062_S23_L007_I1_001.fastq.gz",
1045            "upload_status": "validated"
1046        },
1047        {
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1049            "accession": "IGVFFI3735TQAL",
1050            "aliases": [
1051                "igvf:corces_sequenceFile_RNA_RP013_G3_P062_L008_R1"
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1068        },
1069        {
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1071            "accession": "IGVFFI6574KUBC",
1072            "aliases": [
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1076            "controlled_access": false,
1077            "creation_timestamp": "2025-03-20T21:04:31.155593+00:00",
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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_RNA_RP013_G3_L003_P062_S23_L008_I1_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
1092            "@id": "/sequence-files/IGVFFI3623MMKK/",
1093            "accession": "IGVFFI3623MMKK",
1094            "aliases": [
1095                "igvf:corces_sequenceFile_RNA_RP013_G3_P062_L007_R2"
1096            ],
1097            "content_type": "reads",
1098            "controlled_access": false,
1099            "creation_timestamp": "2025-03-20T21:04:25.998827+00:00",
1100            "file_format": "fastq",
1101            "file_size": 2165503345,
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1103            "s3_uri": "s3://igvf-files/2025/03/20/6e8a96d1-1345-4bae-95d2-1efe1785d867/IGVFFI3623MMKK.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_RNA_RP013_G3_L003_P062_S23_L007_R2_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI3416PWFS/",
1115            "accession": "IGVFFI3416PWFS",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_RNA_RP013_G3_P062_L006_I2"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T21:04:03.292948+00:00",
1122            "file_format": "fastq",
1123            "file_size": 327448542,
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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_G3_L003_P062_S23_L006_I2_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI2308TXQD/",
1137            "accession": "IGVFFI2308TXQD",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_RNA_RP013_G3_P062_L008_R2"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T21:04:43.067756+00:00",
1144            "file_format": "fastq",
1145            "file_size": 2011202329,
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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_RNA_RP013_G3_L003_P062_S23_L008_R2_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI4049CZMX/",
1159            "accession": "IGVFFI4049CZMX",
1160            "aliases": [
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1293        "title": "Ryan Corces, Gladstone Institute UCSF"
1294    },
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1296    "onlist_files": [
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1298    ],
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1300    "preferred_assay_title": "10x multiome",
1301    "protocols": [
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1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
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1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP013_G3"
1322            ],
1323            "classifications": [
1324                "tissue",
1325                "multiplexed sample"
1326            ],
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1330                    "status": "in progress",
1331                    "term_name": "mild cognitive impairment"
1332                },
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1337                },
1338                {
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1341                    "term_name": "multiple sclerosis"
1342                },
1343                {
1344                    "@id": "/phenotype-terms/DOID_9246/",
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1347                },
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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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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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1411            "taxa": "Homo sapiens",
1412            "treatments": []
1413        }
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1420    },
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1422    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
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1424}