IGVFDS5184YEZB

1{
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4    "@type": [
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10    "aliases": [
11        "igvf:corces_measurementSet_RP014_G8_ATAC"
12    ],
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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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689            {
690                "category": "missing sequence specification",
691                "detail": "Measurement set [IGVFDS5184YEZB](/measurement-sets/IGVFDS5184YEZB/) has sequence file(s): [IGVFFI0006NWCC](/sequence-files/IGVFFI0006NWCC/), [IGVFFI0170FWFS](/sequence-files/IGVFFI0170FWFS/), [IGVFFI9862CFBK](/sequence-files/IGVFFI9862CFBK/), [IGVFFI0986ZHIO](/sequence-files/IGVFFI0986ZHIO/), [IGVFFI0036FQZE](/sequence-files/IGVFFI0036FQZE/), [IGVFFI3242TJZO](/sequence-files/IGVFFI3242TJZO/), [IGVFFI9226QRNS](/sequence-files/IGVFFI9226QRNS/), [IGVFFI7953QDHJ](/sequence-files/IGVFFI7953QDHJ/), [IGVFFI5765TGZH](/sequence-files/IGVFFI5765TGZH/), [IGVFFI8577FXGC](/sequence-files/IGVFFI8577FXGC/), [IGVFFI4879SGMZ](/sequence-files/IGVFFI4879SGMZ/), [IGVFFI2978YWOQ](/sequence-files/IGVFFI2978YWOQ/), [IGVFFI4016HKSN](/sequence-files/IGVFFI4016HKSN/), [IGVFFI8297JNLW](/sequence-files/IGVFFI8297JNLW/), [IGVFFI9642JKDT](/sequence-files/IGVFFI9642JKDT/), [IGVFFI5834GPNY](/sequence-files/IGVFFI5834GPNY/) 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.",
692                "level": 50,
693                "level_name": "NOT_COMPLIANT",
694                "name": "audit_missing_seqspec",
695                "path": "/measurement-sets/IGVFDS5184YEZB/"
696            },
697            {
698                "category": "missing strand specificity",
699                "detail": "Measurement set [IGVFDS5184YEZB](/measurement-sets/IGVFDS5184YEZB/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
700                "level": 50,
701                "level_name": "NOT_COMPLIANT",
702                "name": "audit_missing_strand_specificity",
703                "path": "/measurement-sets/IGVFDS5184YEZB/"
704            }
705        ],
706        "WARNING": [
707            {
708                "category": "missing analysis",
709                "detail": "Measurement set [IGVFDS5184YEZB](/measurement-sets/IGVFDS5184YEZB/) 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.",
710                "level": 40,
711                "level_name": "WARNING",
712                "name": "audit_input_for",
713                "path": "/measurement-sets/IGVFDS5184YEZB/"
714            }
715        ]
716    },
717    "award": {
718        "@id": "/awards/HG012076/",
719        "component": "mapping",
720        "contact_pi": {
721            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
722            "title": "Ansuman Satpathy"
723        },
724        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
725    },
726    "control_for": [],
727    "controlled_access": false,
728    "creation_timestamp": "2025-03-19T19:54:51.661559+00:00",
729    "data_use_limitation_summaries": [
730        "No limitations"
731    ],
732    "donors": [
733        {
734            "@id": "/human-donors/IGVFDO1464XWYC/",
735            "accession": "IGVFDO1464XWYC",
736            "aliases": [
737                "igvf:corces_donor_BANN1809"
738            ],
739            "sex": "male",
740            "status": "preview",
741            "taxa": "Homo sapiens"
742        },
743        {
744            "@id": "/human-donors/IGVFDO4015EJFT/",
745            "accession": "IGVFDO4015EJFT",
746            "aliases": [
747                "igvf:corces_donor_BANN0526"
748            ],
749            "sex": "male",
750            "status": "preview",
751            "taxa": "Homo sapiens"
752        },
753        {
754            "@id": "/human-donors/IGVFDO0565OSFT/",
755            "accession": "IGVFDO0565OSFT",
756            "aliases": [
757                "igvf:corces_donor_BANN1805"
758            ],
759            "sex": "male",
760            "status": "preview",
761            "taxa": "Homo sapiens"
762        },
763        {
764            "@id": "/human-donors/IGVFDO7306YMGC/",
765            "accession": "IGVFDO7306YMGC",
766            "aliases": [
767                "igvf:corces_donor_BANN0517"
768            ],
769            "sex": "female",
770            "status": "preview",
771            "taxa": "Homo sapiens"
772        },
773        {
774            "@id": "/human-donors/IGVFDO7678VYKP/",
775            "accession": "IGVFDO7678VYKP",
776            "aliases": [
777                "igvf:corces_donor_BANN1235"
778            ],
779            "sex": "male",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
784            "@id": "/human-donors/IGVFDO0411QFOF/",
785            "accession": "IGVFDO0411QFOF",
786            "aliases": [
787                "igvf:corces_donor_BANN1750"
788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO7732SCUF/",
795            "accession": "IGVFDO7732SCUF",
796            "aliases": [
797                "igvf:corces_donor_BANN0351"
798            ],
799            "sex": "male",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
804            "@id": "/human-donors/IGVFDO7606UOXI/",
805            "accession": "IGVFDO7606UOXI",
806            "aliases": [
807                "igvf:corces_donor_BANN1570"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
814            "@id": "/human-donors/IGVFDO1302YEPX/",
815            "accession": "IGVFDO1302YEPX",
816            "aliases": [
817                "igvf:corces_donor_BANN0215"
818            ],
819            "sex": "female",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
824            "@id": "/human-donors/IGVFDO4191KJBR/",
825            "accession": "IGVFDO4191KJBR",
826            "aliases": [
827                "igvf:corces_donor_BANN0129"
828            ],
829            "sex": "male",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
834            "@id": "/human-donors/IGVFDO9211DWXZ/",
835            "accession": "IGVFDO9211DWXZ",
836            "aliases": [
837                "igvf:corces_donor_BANN1352"
838            ],
839            "sex": "female",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
844            "@id": "/human-donors/IGVFDO4783EEYU/",
845            "accession": "IGVFDO4783EEYU",
846            "aliases": [
847                "igvf:corces_donor_BANN1865"
848            ],
849            "sex": "male",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO4273OHGB/",
855            "accession": "IGVFDO4273OHGB",
856            "aliases": [
857                "igvf:corces_donor_BANN0322"
858            ],
859            "sex": "female",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
864            "@id": "/human-donors/IGVFDO8458OKEW/",
865            "accession": "IGVFDO8458OKEW",
866            "aliases": [
867                "igvf:corces_donor_BANN1623"
868            ],
869            "sex": "male",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
874            "@id": "/human-donors/IGVFDO0966KXTA/",
875            "accession": "IGVFDO0966KXTA",
876            "aliases": [
877                "igvf:corces_donor_BANN0138"
878            ],
879            "sex": "female",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO3911JQLE/",
885            "accession": "IGVFDO3911JQLE",
886            "aliases": [
887                "igvf:corces_donor_BANN1412"
888            ],
889            "sex": "male",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        }
893    ],
894    "externally_hosted": false,
895    "file_set_type": "experimental data",
896    "files": [
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898            "@id": "/sequence-files/IGVFFI0006NWCC/",
899            "accession": "IGVFFI0006NWCC",
900            "aliases": [
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903            "content_type": "reads",
904            "controlled_access": false,
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910            "sequencing_platform": {
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912                "status": "released",
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915            "status": "preview",
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917            "upload_status": "validated"
918        },
919        {
920            "@id": "/sequence-files/IGVFFI0170FWFS/",
921            "accession": "IGVFFI0170FWFS",
922            "aliases": [
923                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L001_R2"
924            ],
925            "content_type": "reads",
926            "controlled_access": false,
927            "creation_timestamp": "2025-03-20T20:33:59.620041+00:00",
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940        },
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943            "accession": "IGVFFI9862CFBK",
944            "aliases": [
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947            "content_type": "reads",
948            "controlled_access": false,
949            "creation_timestamp": "2025-03-20T20:34:29.510325+00:00",
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960            "submitted_file_name": "Multiome_ATAC_RP014_G8_L008_P061_S16_L004_I1_001.fastq.gz",
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963        {
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965            "accession": "IGVFFI0986ZHIO",
966            "aliases": [
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969            "content_type": "reads",
970            "controlled_access": false,
971            "creation_timestamp": "2025-03-20T20:34:34.334258+00:00",
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985        {
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987            "accession": "IGVFFI0036FQZE",
988            "aliases": [
989                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L004_R2"
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993            "creation_timestamp": "2025-03-20T20:34:38.594035+00:00",
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1005            "upload_status": "validated"
1006        },
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1009            "accession": "IGVFFI3242TJZO",
1010            "aliases": [
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1014            "controlled_access": false,
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1028        },
1029        {
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1031            "accession": "IGVFFI9226QRNS",
1032            "aliases": [
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1037            "creation_timestamp": "2025-03-20T20:34:42.683779+00:00",
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1045                "term_name": "Illumina NovaSeq X"
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1049            "upload_status": "validated"
1050        },
1051        {
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1053            "accession": "IGVFFI7953QDHJ",
1054            "aliases": [
1055                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L001_R1"
1056            ],
1057            "content_type": "reads",
1058            "controlled_access": false,
1059            "creation_timestamp": "2025-03-20T20:33:56.427868+00:00",
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1071            "upload_status": "validated"
1072        },
1073        {
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1075            "accession": "IGVFFI5765TGZH",
1076            "aliases": [
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1080            "controlled_access": false,
1081            "creation_timestamp": "2025-03-20T20:34:05.884043+00:00",
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1089                "term_name": "Illumina NovaSeq X"
1090            },
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1093            "upload_status": "validated"
1094        },
1095        {
1096            "@id": "/sequence-files/IGVFFI8577FXGC/",
1097            "accession": "IGVFFI8577FXGC",
1098            "aliases": [
1099                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L001_R3"
1100            ],
1101            "content_type": "reads",
1102            "controlled_access": false,
1103            "creation_timestamp": "2025-03-20T20:34:02.429823+00:00",
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1111                "term_name": "Illumina NovaSeq X"
1112            },
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1114            "submitted_file_name": "Multiome_ATAC_RP014_G8_L008_P061_S16_L001_R3_001.fastq.gz",
1115            "upload_status": "validated"
1116        },
1117        {
1118            "@id": "/sequence-files/IGVFFI4879SGMZ/",
1119            "accession": "IGVFFI4879SGMZ",
1120            "aliases": [
1121                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L002_R1"
1122            ],
1123            "content_type": "reads",
1124            "controlled_access": false,
1125            "creation_timestamp": "2025-03-20T20:34:09.472614+00:00",
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1130            "sequencing_platform": {
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1132                "status": "released",
1133                "term_name": "Illumina NovaSeq X"
1134            },
1135            "status": "preview",
1136            "submitted_file_name": "Multiome_ATAC_RP014_G8_L008_P061_S16_L002_R1_001.fastq.gz",
1137            "upload_status": "validated"
1138        },
1139        {
1140            "@id": "/sequence-files/IGVFFI2978YWOQ/",
1141            "accession": "IGVFFI2978YWOQ",
1142            "aliases": [
1143                "igvf:corces_sequenceFile_ATAC_RP014_G8_P061_L002_R2"
1144            ],
1145            "content_type": "reads",
1146            "controlled_access": false,
1147            "creation_timestamp": "2025-03-20T20:34:11.923140+00:00",
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1251    "lab": {
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1253        "title": "Ryan Corces, Gladstone Institute UCSF"
1254    },
1255    "multiome_size": 2,
1256    "onlist_files": [
1257        "/tabular-files/IGVFFI7587TJLC/"
1258    ],
1259    "onlist_method": "no combination",
1260    "preferred_assay_title": "10x multiome",
1261    "protocols": [
1262        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1263    ],
1264    "related_multiome_datasets": [
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1267            "accession": "IGVFDS3473OBBZ",
1268            "status": "preview"
1269        }
1270    ],
1271    "samples": [
1272        {
1273            "@id": "/multiplexed-samples/IGVFSM7659CCOT/",
1274            "@type": [
1275                "MultiplexedSample",
1276                "Sample",
1277                "Item"
1278            ],
1279            "accession": "IGVFSM7659CCOT",
1280            "aliases": [
1281                "igvf:corces_multiplexedSample_RP014_G8"
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1283            "classifications": [
1284                "tissue",
1285                "multiplexed sample"
1286            ],
1287            "disease_terms": [
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1289                    "@id": "/phenotype-terms/DOID_0080832/",
1290                    "status": "in progress",
1291                    "term_name": "mild cognitive impairment"
1292                },
1293                {
1294                    "@id": "/phenotype-terms/DOID_14330/",
1295                    "status": "in progress",
1296                    "term_name": "Parkinson's disease"
1297                },
1298                {
1299                    "@id": "/phenotype-terms/DOID_9246/",
1300                    "status": "in progress",
1301                    "term_name": "cerebral amyloid angiopathy"
1302                },
1303                {
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1305                    "status": "released",
1306                    "term_name": "Alzheimer disease"
1307                }
1308            ],
1309            "institutional_certificates": [
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1312                    "certificate_identifier": "IP115-05",
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1314                    "status": "in progress"
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1321                    "@type": [
1322                        "SampleTerm",
1323                        "OntologyTerm",
1324                        "Item"
1325                    ],
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1329                },
1330                {
1331                    "@id": "/sample-terms/UBERON_0002038/",
1332                    "@type": [
1333                        "SampleTerm",
1334                        "OntologyTerm",
1335                        "Item"
1336                    ],
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1338                    "summary": "substantia nigra",
1339                    "term_name": "substantia nigra"
1340                },
1341                {
1342                    "@id": "/sample-terms/UBERON_0002740/",
1343                    "@type": [
1344                        "SampleTerm",
1345                        "OntologyTerm",
1346                        "Item"
1347                    ],
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1349                    "summary": "posterior cingulate gyrus",
1350                    "term_name": "posterior cingulate gyrus"
1351                },
1352                {
1353                    "@id": "/sample-terms/UBERON_0002771/",
1354                    "@type": [
1355                        "SampleTerm",
1356                        "OntologyTerm",
1357                        "Item"
1358                    ],
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1362                }
1363            ],
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1366            "taxa": "Homo sapiens",
1367            "treatments": []
1368        }
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1371    "status": "preview",
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1374        "title": "Ryan Corces"
1375    },
1376    "submitted_files_timestamp": "2025-03-20T20:33:53.563853+00:00",
1377    "summary": "single-nucleus ATAC-seq (10x multiome)",
1378    "uuid": "62449aff-20ab-4f26-af9b-7f40719c400f"
1379}