IGVFDS0028AWOA

1{
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3    "@id": "/measurement-sets/IGVFDS0028AWOA/",
4    "@type": [
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10    "aliases": [
11        "igvf:corces_measurementSet_RP013_G7_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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703            {
704                "category": "mismatched status",
705                "detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [d2909f2d-5e28-4e1f-859d-c562f1c883af](/phenotypic-features/d2909f2d-5e28-4e1f-859d-c562f1c883af/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO4108VCBA/"
710            },
711            {
712                "category": "mismatched status",
713                "detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [1bb96444-071d-4a8d-81ef-b6567ef83275](/phenotypic-features/1bb96444-071d-4a8d-81ef-b6567ef83275/).",
714                "level": 30,
715                "level_name": "INTERNAL_ACTION",
716                "name": "audit_item_status",
717                "path": "/human-donors/IGVFDO4108VCBA/"
718            },
719            {
720                "category": "mismatched status",
721                "detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [aff60c46-5191-4203-ac06-8623d7e676fa](/phenotypic-features/aff60c46-5191-4203-ac06-8623d7e676fa/).",
722                "level": 30,
723                "level_name": "INTERNAL_ACTION",
724                "name": "audit_item_status",
725                "path": "/human-donors/IGVFDO4108VCBA/"
726            }
727        ],
728        "NOT_COMPLIANT": [
729            {
730                "category": "missing sequence specification",
731                "detail": "Measurement set [IGVFDS0028AWOA](/measurement-sets/IGVFDS0028AWOA/) has sequence file(s): [IGVFFI9038XNYG](/sequence-files/IGVFFI9038XNYG/), [IGVFFI0301QLVU](/sequence-files/IGVFFI0301QLVU/), [IGVFFI4598NRVM](/sequence-files/IGVFFI4598NRVM/), [IGVFFI1396YQVF](/sequence-files/IGVFFI1396YQVF/), [IGVFFI0758CZQA](/sequence-files/IGVFFI0758CZQA/), [IGVFFI9244UKAS](/sequence-files/IGVFFI9244UKAS/), [IGVFFI3987KSLE](/sequence-files/IGVFFI3987KSLE/), [IGVFFI0254UWKJ](/sequence-files/IGVFFI0254UWKJ/), [IGVFFI5264PCRV](/sequence-files/IGVFFI5264PCRV/), [IGVFFI9904FGXX](/sequence-files/IGVFFI9904FGXX/), [IGVFFI0328CYUP](/sequence-files/IGVFFI0328CYUP/), [IGVFFI1123UWTG](/sequence-files/IGVFFI1123UWTG/), [IGVFFI1041KPSY](/sequence-files/IGVFFI1041KPSY/), [IGVFFI8670RECJ](/sequence-files/IGVFFI8670RECJ/), [IGVFFI0917XGXV](/sequence-files/IGVFFI0917XGXV/), [IGVFFI8410ALYC](/sequence-files/IGVFFI8410ALYC/) 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/IGVFDS0028AWOA/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS0028AWOA](/measurement-sets/IGVFDS0028AWOA/) 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/IGVFDS0028AWOA/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS0028AWOA](/measurement-sets/IGVFDS0028AWOA/) 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/IGVFDS0028AWOA/"
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": "2025-03-19T19:54:29.057990+00:00",
769    "data_use_limitation_summaries": [
770        "No limitations"
771    ],
772    "donors": [
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774            "@id": "/human-donors/IGVFDO7754VJKM/",
775            "accession": "IGVFDO7754VJKM",
776            "aliases": [
777                "igvf:corces_donor_BANN0341"
778            ],
779            "sex": "male",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
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785            "accession": "IGVFDO7315DYIP",
786            "aliases": [
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788            ],
789            "sex": "female",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO8344LUQZ/",
795            "accession": "IGVFDO8344LUQZ",
796            "aliases": [
797                "igvf:corces_donor_BANN0621"
798            ],
799            "sex": "male",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
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805            "accession": "IGVFDO3971UIZC",
806            "aliases": [
807                "igvf:corces_donor_BANN0217"
808            ],
809            "sex": "female",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
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815            "accession": "IGVFDO4170HAEN",
816            "aliases": [
817                "igvf:corces_donor_BANN1864"
818            ],
819            "sex": "male",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
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825            "accession": "IGVFDO4053HEKW",
826            "aliases": [
827                "igvf:corces_donor_BANN1317"
828            ],
829            "sex": "male",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
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835            "accession": "IGVFDO4273OHGB",
836            "aliases": [
837                "igvf:corces_donor_BANN0322"
838            ],
839            "sex": "female",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
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845            "accession": "IGVFDO7606UOXI",
846            "aliases": [
847                "igvf:corces_donor_BANN1570"
848            ],
849            "sex": "male",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO1797DNPW/",
855            "accession": "IGVFDO1797DNPW",
856            "aliases": [
857                "igvf:corces_donor_BANN1827"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
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865            "accession": "IGVFDO4108VCBA",
866            "aliases": [
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868            ],
869            "sex": "male",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
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875            "accession": "IGVFDO5205IAEO",
876            "aliases": [
877                "igvf:corces_donor_BANN1632"
878            ],
879            "sex": "male",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO8670MHXE/",
885            "accession": "IGVFDO8670MHXE",
886            "aliases": [
887                "igvf:corces_donor_BANN0874"
888            ],
889            "sex": "female",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        },
893        {
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895            "accession": "IGVFDO8800RKVB",
896            "aliases": [
897                "igvf:corces_donor_BANN1872"
898            ],
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900            "status": "preview",
901            "taxa": "Homo sapiens"
902        },
903        {
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905            "accession": "IGVFDO8155MCUV",
906            "aliases": [
907                "igvf:corces_donor_BANN0437"
908            ],
909            "sex": "female",
910            "status": "preview",
911            "taxa": "Homo sapiens"
912        },
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915            "accession": "IGVFDO0180JQCL",
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918            ],
919            "sex": "female",
920            "status": "preview",
921            "taxa": "Homo sapiens"
922        },
923        {
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925            "accession": "IGVFDO0698ZMAQ",
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928            ],
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930            "status": "preview",
931            "taxa": "Homo sapiens"
932        }
933    ],
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940            "aliases": [
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953                "term_name": "Illumina NovaSeq X"
954            },
955            "status": "preview",
956            "submitted_file_name": "Multiome_ATAC_RP013_G7_L007_P061_S7_L004_R3_001.fastq.gz",
957            "upload_status": "validated"
958        },
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967            "creation_timestamp": "2025-03-20T20:26:24.755058+00:00",
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978            "submitted_file_name": "Multiome_ATAC_RP013_G7_L007_P061_S7_L004_R1_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": "2025-03-20T20:25:49.525332+00:00",
990            "file_format": "fastq",
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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_ATAC_RP013_G7_L007_P061_S7_L001_R3_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
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1005            "accession": "IGVFFI1396YQVF",
1006            "aliases": [
1007                "igvf:corces_sequenceFile_ATAC_RP013_G7_P061_L002_R2"
1008            ],
1009            "content_type": "reads",
1010            "controlled_access": false,
1011            "creation_timestamp": "2025-03-20T20:25:59.921424+00:00",
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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_ATAC_RP013_G7_L007_P061_S7_L002_R2_001.fastq.gz",
1023            "upload_status": "validated"
1024        },
1025        {
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1027            "accession": "IGVFFI0758CZQA",
1028            "aliases": [
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1031            "content_type": "reads",
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1033            "creation_timestamp": "2025-03-20T20:25:39.885300+00:00",
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1038            "sequencing_platform": {
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1041                "term_name": "Illumina NovaSeq X"
1042            },
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1044            "submitted_file_name": "Multiome_ATAC_RP013_G7_L007_P061_S7_L001_I1_001.fastq.gz",
1045            "upload_status": "validated"
1046        },
1047        {
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1049            "accession": "IGVFFI9244UKAS",
1050            "aliases": [
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1052            ],
1053            "content_type": "reads",
1054            "controlled_access": false,
1055            "creation_timestamp": "2025-03-20T20:25:42.967420+00:00",
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1060            "sequencing_platform": {
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1064            },
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1067            "upload_status": "validated"
1068        },
1069        {
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1071            "accession": "IGVFFI3987KSLE",
1072            "aliases": [
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1074            ],
1075            "content_type": "reads",
1076            "controlled_access": false,
1077            "creation_timestamp": "2025-03-20T20:25:46.331747+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_ATAC_RP013_G7_L007_P061_S7_L001_R2_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
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1093            "accession": "IGVFFI0254UWKJ",
1094            "aliases": [
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1096            ],
1097            "content_type": "reads",
1098            "controlled_access": false,
1099            "creation_timestamp": "2025-03-20T20:25:53.612141+00:00",
1100            "file_format": "fastq",
1101            "file_size": 454247938,
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1103            "s3_uri": "s3://igvf-files/2025/03/20/bcbab7e7-88db-41b6-bb86-98bb6ca1421b/IGVFFI0254UWKJ.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_G7_L007_P061_S7_L002_I1_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI5264PCRV/",
1115            "accession": "IGVFFI5264PCRV",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_ATAC_RP013_G7_P061_L002_R3"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T20:26:03.126315+00:00",
1122            "file_format": "fastq",
1123            "file_size": 1848917911,
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1125            "s3_uri": "s3://igvf-files/2025/03/20/d55a88ae-2e21-4a26-91e8-c6902779ff22/IGVFFI5264PCRV.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_G7_L007_P061_S7_L002_R3_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI9904FGXX/",
1137            "accession": "IGVFFI9904FGXX",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_ATAC_RP013_G7_P061_L003_I1"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T20:26:07.057535+00:00",
1144            "file_format": "fastq",
1145            "file_size": 452686320,
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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_ATAC_RP013_G7_L007_P061_S7_L003_I1_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI0328CYUP/",
1159            "accession": "IGVFFI0328CYUP",
1160            "aliases": [
1161                "igvf:corces_sequenceFile_ATAC_RP013_G7_P061_L003_R1"
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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": [
1302        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
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1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
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1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP013_G7"
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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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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                {
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1350                    "status": "released",
1351                    "term_name": "Alzheimer disease"
1352                }
1353            ],
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1357                    "certificate_identifier": "IP115-05",
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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                {
1387                    "@id": "/sample-terms/UBERON_0002740/",
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                }
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1411            "taxa": "Homo sapiens",
1412            "treatments": []
1413        }
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1419        "title": "Ryan Corces"
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1421    "submitted_files_timestamp": "2025-03-20T20:25:39.885300+00:00",
1422    "summary": "single-nucleus ATAC-seq (10x multiome)",
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1424}