IGVFDS9129KQZH

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703            {
704                "category": "mismatched status",
705                "detail": "Preview human donor [IGVFDO8451NMBP](/human-donors/IGVFDO8451NMBP/) has in progress subobject phenotypic feature [5aadb7a0-3ba4-46ce-a63b-737069e87fe2](/phenotypic-features/5aadb7a0-3ba4-46ce-a63b-737069e87fe2/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO8451NMBP/"
710            }
711        ],
712        "NOT_COMPLIANT": [
713            {
714                "category": "missing sequence specification",
715                "detail": "Measurement set [IGVFDS9129KQZH](/measurement-sets/IGVFDS9129KQZH/) has sequence file(s): [IGVFFI1001UUBC](/sequence-files/IGVFFI1001UUBC/), [IGVFFI5810VKRE](/sequence-files/IGVFFI5810VKRE/), [IGVFFI3396QAHR](/sequence-files/IGVFFI3396QAHR/), [IGVFFI0152GUIK](/sequence-files/IGVFFI0152GUIK/), [IGVFFI5836CEVG](/sequence-files/IGVFFI5836CEVG/), [IGVFFI4065LZMW](/sequence-files/IGVFFI4065LZMW/), [IGVFFI6634TTGD](/sequence-files/IGVFFI6634TTGD/), [IGVFFI7989CMYP](/sequence-files/IGVFFI7989CMYP/), [IGVFFI1759KABX](/sequence-files/IGVFFI1759KABX/), [IGVFFI1189JSIK](/sequence-files/IGVFFI1189JSIK/), [IGVFFI7849UYSQ](/sequence-files/IGVFFI7849UYSQ/), [IGVFFI5548OTNG](/sequence-files/IGVFFI5548OTNG/), [IGVFFI6026ZMUA](/sequence-files/IGVFFI6026ZMUA/), [IGVFFI2296CSKM](/sequence-files/IGVFFI2296CSKM/), [IGVFFI2931GFLY](/sequence-files/IGVFFI2931GFLY/), [IGVFFI8924VSZB](/sequence-files/IGVFFI8924VSZB/) 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.",
716                "level": 50,
717                "level_name": "NOT_COMPLIANT",
718                "name": "audit_missing_seqspec",
719                "path": "/measurement-sets/IGVFDS9129KQZH/"
720            },
721            {
722                "category": "missing strand specificity",
723                "detail": "Measurement set [IGVFDS9129KQZH](/measurement-sets/IGVFDS9129KQZH/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
724                "level": 50,
725                "level_name": "NOT_COMPLIANT",
726                "name": "audit_missing_strand_specificity",
727                "path": "/measurement-sets/IGVFDS9129KQZH/"
728            }
729        ],
730        "WARNING": [
731            {
732                "category": "missing analysis",
733                "detail": "Measurement set [IGVFDS9129KQZH](/measurement-sets/IGVFDS9129KQZH/) 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.",
734                "level": 40,
735                "level_name": "WARNING",
736                "name": "audit_input_for",
737                "path": "/measurement-sets/IGVFDS9129KQZH/"
738            }
739        ]
740    },
741    "award": {
742        "@id": "/awards/HG012076/",
743        "component": "mapping",
744        "contact_pi": {
745            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
746            "title": "Ansuman Satpathy"
747        },
748        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
749    },
750    "control_for": [],
751    "controlled_access": false,
752    "creation_timestamp": "2025-03-19T21:42:31.128299+00:00",
753    "data_use_limitation_summaries": [
754        "No limitations"
755    ],
756    "donors": [
757        {
758            "@id": "/human-donors/IGVFDO2559GIIZ/",
759            "accession": "IGVFDO2559GIIZ",
760            "aliases": [
761                "igvf:corces_donor_BANN2103"
762            ],
763            "sex": "male",
764            "status": "preview",
765            "taxa": "Homo sapiens"
766        },
767        {
768            "@id": "/human-donors/IGVFDO4053HEKW/",
769            "accession": "IGVFDO4053HEKW",
770            "aliases": [
771                "igvf:corces_donor_BANN1317"
772            ],
773            "sex": "male",
774            "status": "preview",
775            "taxa": "Homo sapiens"
776        },
777        {
778            "@id": "/human-donors/IGVFDO6013FYCW/",
779            "accession": "IGVFDO6013FYCW",
780            "aliases": [
781                "igvf:corces_donor_BANN0912"
782            ],
783            "sex": "male",
784            "status": "preview",
785            "taxa": "Homo sapiens"
786        },
787        {
788            "@id": "/human-donors/IGVFDO7754VJKM/",
789            "accession": "IGVFDO7754VJKM",
790            "aliases": [
791                "igvf:corces_donor_BANN0341"
792            ],
793            "sex": "male",
794            "status": "preview",
795            "taxa": "Homo sapiens"
796        },
797        {
798            "@id": "/human-donors/IGVFDO8547HLIG/",
799            "accession": "IGVFDO8547HLIG",
800            "aliases": [
801                "igvf:corces_donor_BANN1812"
802            ],
803            "sex": "female",
804            "status": "preview",
805            "taxa": "Homo sapiens"
806        },
807        {
808            "@id": "/human-donors/IGVFDO4783EEYU/",
809            "accession": "IGVFDO4783EEYU",
810            "aliases": [
811                "igvf:corces_donor_BANN1865"
812            ],
813            "sex": "male",
814            "status": "preview",
815            "taxa": "Homo sapiens"
816        },
817        {
818            "@id": "/human-donors/IGVFDO8800RKVB/",
819            "accession": "IGVFDO8800RKVB",
820            "aliases": [
821                "igvf:corces_donor_BANN1872"
822            ],
823            "sex": "female",
824            "status": "preview",
825            "taxa": "Homo sapiens"
826        },
827        {
828            "@id": "/human-donors/IGVFDO5718REZU/",
829            "accession": "IGVFDO5718REZU",
830            "aliases": [
831                "igvf:corces_donor_BANN9926"
832            ],
833            "sex": "female",
834            "status": "preview",
835            "taxa": "Homo sapiens"
836        },
837        {
838            "@id": "/human-donors/IGVFDO0909BNTN/",
839            "accession": "IGVFDO0909BNTN",
840            "aliases": [
841                "igvf:corces_donor_BANN1554"
842            ],
843            "sex": "male",
844            "status": "preview",
845            "taxa": "Homo sapiens"
846        },
847        {
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849            "accession": "IGVFDO7109IWDJ",
850            "aliases": [
851                "igvf:corces_donor_BANN2005"
852            ],
853            "sex": "male",
854            "status": "preview",
855            "taxa": "Homo sapiens"
856        },
857        {
858            "@id": "/human-donors/IGVFDO7606UOXI/",
859            "accession": "IGVFDO7606UOXI",
860            "aliases": [
861                "igvf:corces_donor_BANN1570"
862            ],
863            "sex": "male",
864            "status": "preview",
865            "taxa": "Homo sapiens"
866        },
867        {
868            "@id": "/human-donors/IGVFDO1797DNPW/",
869            "accession": "IGVFDO1797DNPW",
870            "aliases": [
871                "igvf:corces_donor_BANN1827"
872            ],
873            "sex": "male",
874            "status": "preview",
875            "taxa": "Homo sapiens"
876        },
877        {
878            "@id": "/human-donors/IGVFDO1464XWYC/",
879            "accession": "IGVFDO1464XWYC",
880            "aliases": [
881                "igvf:corces_donor_BANN1809"
882            ],
883            "sex": "male",
884            "status": "preview",
885            "taxa": "Homo sapiens"
886        },
887        {
888            "@id": "/human-donors/IGVFDO5205IAEO/",
889            "accession": "IGVFDO5205IAEO",
890            "aliases": [
891                "igvf:corces_donor_BANN1632"
892            ],
893            "sex": "male",
894            "status": "preview",
895            "taxa": "Homo sapiens"
896        },
897        {
898            "@id": "/human-donors/IGVFDO5214IKNF/",
899            "accession": "IGVFDO5214IKNF",
900            "aliases": [
901                "igvf:corces_donor_BANN1070"
902            ],
903            "sex": "male",
904            "status": "preview",
905            "taxa": "Homo sapiens"
906        },
907        {
908            "@id": "/human-donors/IGVFDO8451NMBP/",
909            "accession": "IGVFDO8451NMBP",
910            "aliases": [
911                "igvf:corces_donor_BANN1756"
912            ],
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914            "status": "preview",
915            "taxa": "Homo sapiens"
916        }
917    ],
918    "externally_hosted": false,
919    "file_set_type": "experimental data",
920    "files": [
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924            "aliases": [
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927            "content_type": "reads",
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940            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L008_R1_001.fastq.gz",
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942        },
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945            "accession": "IGVFFI5810VKRE",
946            "aliases": [
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948            ],
949            "content_type": "reads",
950            "controlled_access": false,
951            "creation_timestamp": "2025-03-20T17:21:57.659312+00:00",
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956            "sequencing_platform": {
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971            "content_type": "reads",
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973            "creation_timestamp": "2025-03-20T17:21:49.297151+00:00",
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978            "sequencing_platform": {
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980                "status": "released",
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984            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L006_I1_001.fastq.gz",
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986        },
987        {
988            "@id": "/sequence-files/IGVFFI0152GUIK/",
989            "accession": "IGVFFI0152GUIK",
990            "aliases": [
991                "igvf:corces_sequenceFile_RNA_RP012_G1_P060_L005_I2"
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993            "content_type": "reads",
994            "controlled_access": false,
995            "creation_timestamp": "2025-03-20T17:21:37.236465+00:00",
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1002                "status": "released",
1003                "term_name": "Illumina NovaSeq X"
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1007            "upload_status": "validated"
1008        },
1009        {
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1011            "accession": "IGVFFI5836CEVG",
1012            "aliases": [
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1016            "controlled_access": false,
1017            "creation_timestamp": "2025-03-20T17:21:54.066425+00:00",
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1024                "status": "released",
1025                "term_name": "Illumina NovaSeq X"
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1028            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L006_I2_001.fastq.gz",
1029            "upload_status": "validated"
1030        },
1031        {
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1033            "accession": "IGVFFI4065LZMW",
1034            "aliases": [
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1037            "content_type": "reads",
1038            "controlled_access": false,
1039            "creation_timestamp": "2025-03-20T17:22:06.434082+00:00",
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1052        },
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1055            "accession": "IGVFFI6634TTGD",
1056            "aliases": [
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1068                "status": "released",
1069                "term_name": "Illumina NovaSeq X"
1070            },
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1072            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L005_I1_001.fastq.gz",
1073            "upload_status": "validated"
1074        },
1075        {
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1078            "aliases": [
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1080            ],
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1083            "creation_timestamp": "2025-03-20T17:21:40.804716+00:00",
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1088            "sequencing_platform": {
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1090                "status": "released",
1091                "term_name": "Illumina NovaSeq X"
1092            },
1093            "status": "preview",
1094            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L005_R1_001.fastq.gz",
1095            "upload_status": "validated"
1096        },
1097        {
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1099            "accession": "IGVFFI1759KABX",
1100            "aliases": [
1101                "igvf:corces_sequenceFile_RNA_RP012_G1_P060_L005_R2"
1102            ],
1103            "content_type": "reads",
1104            "controlled_access": false,
1105            "creation_timestamp": "2025-03-20T17:21:44.847886+00:00",
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1110            "sequencing_platform": {
1111                "@id": "/platform-terms/EFO_0022840/",
1112                "status": "released",
1113                "term_name": "Illumina NovaSeq X"
1114            },
1115            "status": "preview",
1116            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L005_R2_001.fastq.gz",
1117            "upload_status": "validated"
1118        },
1119        {
1120            "@id": "/sequence-files/IGVFFI1189JSIK/",
1121            "accession": "IGVFFI1189JSIK",
1122            "aliases": [
1123                "igvf:corces_sequenceFile_RNA_RP012_G1_P060_L006_R2"
1124            ],
1125            "content_type": "reads",
1126            "controlled_access": false,
1127            "creation_timestamp": "2025-03-20T17:22:02.122892+00:00",
1128            "file_format": "fastq",
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1132            "sequencing_platform": {
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1134                "status": "released",
1135                "term_name": "Illumina NovaSeq X"
1136            },
1137            "status": "preview",
1138            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L006_R2_001.fastq.gz",
1139            "upload_status": "validated"
1140        },
1141        {
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1143            "accession": "IGVFFI7849UYSQ",
1144            "aliases": [
1145                "igvf:corces_sequenceFile_RNA_RP012_G1_P060_L007_I2"
1146            ],
1147            "content_type": "reads",
1148            "controlled_access": false,
1149            "creation_timestamp": "2025-03-20T17:22:12.032507+00:00",
1150            "file_format": "fastq",
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1154            "sequencing_platform": {
1155                "@id": "/platform-terms/EFO_0022840/",
1156                "status": "released",
1157                "term_name": "Illumina NovaSeq X"
1158            },
1159            "status": "preview",
1160            "submitted_file_name": "Multiome_RNA_RP012_G1_L001_P060_S33_L007_I2_001.fastq.gz",
1161            "upload_status": "validated"
1162        },
1163        {
1164            "@id": "/sequence-files/IGVFFI5548OTNG/",
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1254            "aliases": [
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1275    "lab": {
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1277        "title": "Ryan Corces, Gladstone Institute UCSF"
1278    },
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1280    "onlist_files": [
1281        "/tabular-files/IGVFFI8751YQRY/"
1282    ],
1283    "onlist_method": "no combination",
1284    "preferred_assay_title": "10x multiome",
1285    "protocols": [
1286        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1287    ],
1288    "related_multiome_datasets": [
1289        {
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1291            "accession": "IGVFDS8336JFEI",
1292            "status": "preview"
1293        }
1294    ],
1295    "samples": [
1296        {
1297            "@id": "/multiplexed-samples/IGVFSM3122KACM/",
1298            "@type": [
1299                "MultiplexedSample",
1300                "Sample",
1301                "Item"
1302            ],
1303            "accession": "IGVFSM3122KACM",
1304            "aliases": [
1305                "igvf:corces_multiplexedSample_RP012_G1"
1306            ],
1307            "classifications": [
1308                "tissue",
1309                "multiplexed sample"
1310            ],
1311            "disease_terms": [
1312                {
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1314                    "status": "in progress",
1315                    "term_name": "mild cognitive impairment"
1316                },
1317                {
1318                    "@id": "/phenotype-terms/DOID_14330/",
1319                    "status": "in progress",
1320                    "term_name": "Parkinson's disease"
1321                },
1322                {
1323                    "@id": "/phenotype-terms/DOID_9246/",
1324                    "status": "in progress",
1325                    "term_name": "cerebral amyloid angiopathy"
1326                }
1327            ],
1328            "institutional_certificates": [
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1337            "sample_terms": [
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1340                    "@type": [
1341                        "SampleTerm",
1342                        "OntologyTerm",
1343                        "Item"
1344                    ],
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1346                    "summary": "putamen",
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1348                },
1349                {
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1351                    "@type": [
1352                        "SampleTerm",
1353                        "OntologyTerm",
1354                        "Item"
1355                    ],
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1358                    "term_name": "substantia nigra"
1359                },
1360                {
1361                    "@id": "/sample-terms/UBERON_0002129/",
1362                    "@type": [
1363                        "SampleTerm",
1364                        "OntologyTerm",
1365                        "Item"
1366                    ],
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1368                    "summary": "cerebellar cortex",
1369                    "term_name": "cerebellar cortex"
1370                },
1371                {
1372                    "@id": "/sample-terms/UBERON_0002740/",
1373                    "@type": [
1374                        "SampleTerm",
1375                        "OntologyTerm",
1376                        "Item"
1377                    ],
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1379                    "summary": "posterior cingulate gyrus",
1380                    "term_name": "posterior cingulate gyrus"
1381                },
1382                {
1383                    "@id": "/sample-terms/UBERON_0002771/",
1384                    "@type": [
1385                        "SampleTerm",
1386                        "OntologyTerm",
1387                        "Item"
1388                    ],
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1391                    "term_name": "middle temporal gyrus"
1392                }
1393            ],
1394            "status": "preview",
1395            "summary": "multiplexed sample: Homo sapiens (female, 79 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (male, 89 years) substantia nigra tissue; ... and 14 more samples",
1396            "taxa": "Homo sapiens",
1397            "treatments": []
1398        }
1399    ],
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1401    "status": "preview",
1402    "submitted_by": {
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1404        "title": "Ryan Corces"
1405    },
1406    "submitted_files_timestamp": "2025-03-20T17:21:33.423433+00:00",
1407    "summary": "single-nucleus RNA sequencing assay (10x multiome)",
1408    "uuid": "9dd808db-5548-4562-be87-5109068cc435"
1409}