IGVFDS3602NEYS

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS3602NEYS/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS3602NEYS",
10    "aliases": [
11        "igvf:corces_measurementSet_RP011_G5_ATAC"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0002762/",
15        "assay_slims": [
16            "chromatin accessibility"
17        ],
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 [IGVFDS3602NEYS](/measurement-sets/IGVFDS3602NEYS/) has sequence file(s): [IGVFFI2501NLON](/sequence-files/IGVFFI2501NLON/), [IGVFFI4896MQFJ](/sequence-files/IGVFFI4896MQFJ/), [IGVFFI1221FWOL](/sequence-files/IGVFFI1221FWOL/), [IGVFFI7087GFTF](/sequence-files/IGVFFI7087GFTF/), [IGVFFI7517ORAR](/sequence-files/IGVFFI7517ORAR/), [IGVFFI2549DYRL](/sequence-files/IGVFFI2549DYRL/), [IGVFFI7136VYTY](/sequence-files/IGVFFI7136VYTY/), [IGVFFI5510SZWK](/sequence-files/IGVFFI5510SZWK/), [IGVFFI1740TPKK](/sequence-files/IGVFFI1740TPKK/), [IGVFFI3074POYB](/sequence-files/IGVFFI3074POYB/), [IGVFFI0313DQUL](/sequence-files/IGVFFI0313DQUL/), [IGVFFI5676UKKS](/sequence-files/IGVFFI5676UKKS/), [IGVFFI9712JUDH](/sequence-files/IGVFFI9712JUDH/), [IGVFFI3821RLDU](/sequence-files/IGVFFI3821RLDU/), [IGVFFI0897AUML](/sequence-files/IGVFFI0897AUML/), [IGVFFI7106SMXS](/sequence-files/IGVFFI7106SMXS/) 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/IGVFDS3602NEYS/"
696            },
697            {
698                "category": "missing strand specificity",
699                "detail": "Measurement set [IGVFDS3602NEYS](/measurement-sets/IGVFDS3602NEYS/) 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/IGVFDS3602NEYS/"
704            }
705        ],
706        "WARNING": [
707            {
708                "category": "missing analysis",
709                "detail": "Measurement set [IGVFDS3602NEYS](/measurement-sets/IGVFDS3602NEYS/) 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/IGVFDS3602NEYS/"
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": "2025-03-19T19:53:45.712824+00:00",
729    "data_use_limitation_summaries": [
730        "No limitations"
731    ],
732    "donors": [
733        {
734            "@id": "/human-donors/IGVFDO3497MBPK/",
735            "accession": "IGVFDO3497MBPK",
736            "aliases": [
737                "igvf:corces_donor_BANN0002"
738            ],
739            "sex": "male",
740            "status": "preview",
741            "taxa": "Homo sapiens"
742        },
743        {
744            "@id": "/human-donors/IGVFDO7227BIXW/",
745            "accession": "IGVFDO7227BIXW",
746            "aliases": [
747                "igvf:corces_donor_BANN1614"
748            ],
749            "sex": "male",
750            "status": "preview",
751            "taxa": "Homo sapiens"
752        },
753        {
754            "@id": "/human-donors/IGVFDO0773NPOH/",
755            "accession": "IGVFDO0773NPOH",
756            "aliases": [
757                "igvf:corces_donor_BANN0560"
758            ],
759            "sex": "male",
760            "status": "preview",
761            "taxa": "Homo sapiens"
762        },
763        {
764            "@id": "/human-donors/IGVFDO1469WVVS/",
765            "accession": "IGVFDO1469WVVS",
766            "aliases": [
767                "igvf:corces_donor_BANN1063"
768            ],
769            "sex": "male",
770            "status": "preview",
771            "taxa": "Homo sapiens"
772        },
773        {
774            "@id": "/human-donors/IGVFDO1797DNPW/",
775            "accession": "IGVFDO1797DNPW",
776            "aliases": [
777                "igvf:corces_donor_BANN1827"
778            ],
779            "sex": "male",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
784            "@id": "/human-donors/IGVFDO2928PSUK/",
785            "accession": "IGVFDO2928PSUK",
786            "aliases": [
787                "igvf:corces_donor_BANN0950"
788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO5228HTJC/",
795            "accession": "IGVFDO5228HTJC",
796            "aliases": [
797                "igvf:corces_donor_BANN1839"
798            ],
799            "sex": "female",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
804            "@id": "/human-donors/IGVFDO3501RYHX/",
805            "accession": "IGVFDO3501RYHX",
806            "aliases": [
807                "igvf:corces_donor_BANN1959"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
814            "@id": "/human-donors/IGVFDO7649CIGW/",
815            "accession": "IGVFDO7649CIGW",
816            "aliases": [
817                "igvf:corces_donor_BANN9902"
818            ],
819            "sex": "female",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
824            "@id": "/human-donors/IGVFDO1997RFPJ/",
825            "accession": "IGVFDO1997RFPJ",
826            "aliases": [
827                "igvf:corces_donor_BANN1340"
828            ],
829            "sex": "male",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
834            "@id": "/human-donors/IGVFDO2028IGVN/",
835            "accession": "IGVFDO2028IGVN",
836            "aliases": [
837                "igvf:corces_donor_BANN1256"
838            ],
839            "sex": "female",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
844            "@id": "/human-donors/IGVFDO8670MHXE/",
845            "accession": "IGVFDO8670MHXE",
846            "aliases": [
847                "igvf:corces_donor_BANN0874"
848            ],
849            "sex": "female",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO9247BEUS/",
855            "accession": "IGVFDO9247BEUS",
856            "aliases": [
857                "igvf:corces_donor_BANN2149"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
864            "@id": "/human-donors/IGVFDO7720JNYZ/",
865            "accession": "IGVFDO7720JNYZ",
866            "aliases": [
867                "igvf:corces_donor_BANN0438"
868            ],
869            "sex": "female",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
874            "@id": "/human-donors/IGVFDO7186XJLL/",
875            "accession": "IGVFDO7186XJLL",
876            "aliases": [
877                "igvf:corces_donor_BANN1639"
878            ],
879            "sex": "male",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO0698ZMAQ/",
885            "accession": "IGVFDO0698ZMAQ",
886            "aliases": [
887                "igvf:corces_donor_BANN1569"
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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899            "accession": "IGVFFI2501NLON",
900            "aliases": [
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903            "content_type": "reads",
904            "controlled_access": false,
905            "creation_timestamp": "2025-03-20T17:55:19.961407+00:00",
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907            "file_size": 356851355,
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910            "sequencing_platform": {
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912                "status": "released",
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915            "status": "preview",
916            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L006_I1_001.fastq.gz",
917            "upload_status": "validated"
918        },
919        {
920            "@id": "/sequence-files/IGVFFI4896MQFJ/",
921            "accession": "IGVFFI4896MQFJ",
922            "aliases": [
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924            ],
925            "content_type": "reads",
926            "controlled_access": false,
927            "creation_timestamp": "2025-03-20T17:55:54.087670+00:00",
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940        },
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943            "accession": "IGVFFI1221FWOL",
944            "aliases": [
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947            "content_type": "reads",
948            "controlled_access": false,
949            "creation_timestamp": "2025-03-20T17:55:38.246839+00:00",
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956                "status": "released",
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959            "status": "preview",
960            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L007_R1_001.fastq.gz",
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962        },
963        {
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965            "accession": "IGVFFI7087GFTF",
966            "aliases": [
967                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L007_I1"
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969            "content_type": "reads",
970            "controlled_access": false,
971            "creation_timestamp": "2025-03-20T17:55:35.139135+00:00",
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983            "upload_status": "validated"
984        },
985        {
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987            "accession": "IGVFFI7517ORAR",
988            "aliases": [
989                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L005_I1"
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991            "content_type": "reads",
992            "controlled_access": false,
993            "creation_timestamp": "2025-03-20T17:55:04.389807+00:00",
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1001                "term_name": "Illumina NovaSeq X"
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1005            "upload_status": "validated"
1006        },
1007        {
1008            "@id": "/sequence-files/IGVFFI2549DYRL/",
1009            "accession": "IGVFFI2549DYRL",
1010            "aliases": [
1011                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L005_R2"
1012            ],
1013            "content_type": "reads",
1014            "controlled_access": false,
1015            "creation_timestamp": "2025-03-20T17:55:12.634556+00:00",
1016            "file_format": "fastq",
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1027            "upload_status": "validated"
1028        },
1029        {
1030            "@id": "/sequence-files/IGVFFI7136VYTY/",
1031            "accession": "IGVFFI7136VYTY",
1032            "aliases": [
1033                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L005_R1"
1034            ],
1035            "content_type": "reads",
1036            "controlled_access": false,
1037            "creation_timestamp": "2025-03-20T17:55:08.762739+00:00",
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1045                "term_name": "Illumina NovaSeq X"
1046            },
1047            "status": "preview",
1048            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L005_R1_001.fastq.gz",
1049            "upload_status": "validated"
1050        },
1051        {
1052            "@id": "/sequence-files/IGVFFI5510SZWK/",
1053            "accession": "IGVFFI5510SZWK",
1054            "aliases": [
1055                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L005_R3"
1056            ],
1057            "content_type": "reads",
1058            "controlled_access": false,
1059            "creation_timestamp": "2025-03-20T17:55:16.054478+00:00",
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1064            "sequencing_platform": {
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1067                "term_name": "Illumina NovaSeq X"
1068            },
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1070            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L005_R3_001.fastq.gz",
1071            "upload_status": "validated"
1072        },
1073        {
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1075            "accession": "IGVFFI1740TPKK",
1076            "aliases": [
1077                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L006_R3"
1078            ],
1079            "content_type": "reads",
1080            "controlled_access": false,
1081            "creation_timestamp": "2025-03-20T17:55:31.456873+00:00",
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1089                "term_name": "Illumina NovaSeq X"
1090            },
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1092            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L006_R3_001.fastq.gz",
1093            "upload_status": "validated"
1094        },
1095        {
1096            "@id": "/sequence-files/IGVFFI3074POYB/",
1097            "accession": "IGVFFI3074POYB",
1098            "aliases": [
1099                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L007_R3"
1100            ],
1101            "content_type": "reads",
1102            "controlled_access": false,
1103            "creation_timestamp": "2025-03-20T17:55:45.297993+00:00",
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1108            "sequencing_platform": {
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1111                "term_name": "Illumina NovaSeq X"
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1114            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L007_R3_001.fastq.gz",
1115            "upload_status": "validated"
1116        },
1117        {
1118            "@id": "/sequence-files/IGVFFI0313DQUL/",
1119            "accession": "IGVFFI0313DQUL",
1120            "aliases": [
1121                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L008_I1"
1122            ],
1123            "content_type": "reads",
1124            "controlled_access": false,
1125            "creation_timestamp": "2025-03-20T17:55:49.657854+00:00",
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1130            "sequencing_platform": {
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1133                "term_name": "Illumina NovaSeq X"
1134            },
1135            "status": "preview",
1136            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L008_I1_001.fastq.gz",
1137            "upload_status": "validated"
1138        },
1139        {
1140            "@id": "/sequence-files/IGVFFI5676UKKS/",
1141            "accession": "IGVFFI5676UKKS",
1142            "aliases": [
1143                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L008_R2"
1144            ],
1145            "content_type": "reads",
1146            "controlled_access": false,
1147            "creation_timestamp": "2025-03-20T17:55:58.456015+00:00",
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1221                "term_name": "Illumina NovaSeq X"
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1226        },
1227        {
1228            "@id": "/sequence-files/IGVFFI7106SMXS/",
1229            "accession": "IGVFFI7106SMXS",
1230            "aliases": [
1231                "igvf:corces_sequenceFile_ATAC_RP011_G5_P059_L007_R2"
1232            ],
1233            "content_type": "reads",
1234            "controlled_access": false,
1235            "creation_timestamp": "2025-03-20T17:55:42.046968+00:00",
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1246            "submitted_file_name": "Multiome_ATAC_RP011_G5_L005_P059_S77_L007_R2_001.fastq.gz",
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1248        }
1249    ],
1250    "input_for": [],
1251    "lab": {
1252        "@id": "/labs/ryan-corces/",
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": [
1265        {
1266            "@id": "/measurement-sets/IGVFDS3484DNVB/",
1267            "accession": "IGVFDS3484DNVB",
1268            "status": "preview"
1269        }
1270    ],
1271    "samples": [
1272        {
1273            "@id": "/multiplexed-samples/IGVFSM0643EUKR/",
1274            "@type": [
1275                "MultiplexedSample",
1276                "Sample",
1277                "Item"
1278            ],
1279            "accession": "IGVFSM0643EUKR",
1280            "aliases": [
1281                "igvf:corces_multiplexedSample_RP011_G5"
1282            ],
1283            "classifications": [
1284                "tissue",
1285                "multiplexed sample"
1286            ],
1287            "disease_terms": [
1288                {
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                {
1304                    "@id": "/phenotype-terms/MONDO_0004975/",
1305                    "status": "released",
1306                    "term_name": "Alzheimer disease"
1307                }
1308            ],
1309            "institutional_certificates": [
1310                {
1311                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
1312                    "certificate_identifier": "IP115-05",
1313                    "controlled_access": false,
1314                    "status": "in progress"
1315                }
1316            ],
1317            "modifications": [],
1318            "sample_terms": [
1319                {
1320                    "@id": "/sample-terms/UBERON_0001874/",
1321                    "@type": [
1322                        "SampleTerm",
1323                        "OntologyTerm",
1324                        "Item"
1325                    ],
1326                    "status": "preview",
1327                    "summary": "putamen",
1328                    "term_name": "putamen"
1329                },
1330                {
1331                    "@id": "/sample-terms/UBERON_0002038/",
1332                    "@type": [
1333                        "SampleTerm",
1334                        "OntologyTerm",
1335                        "Item"
1336                    ],
1337                    "status": "preview",
1338                    "summary": "substantia nigra",
1339                    "term_name": "substantia nigra"
1340                },
1341                {
1342                    "@id": "/sample-terms/UBERON_0002129/",
1343                    "@type": [
1344                        "SampleTerm",
1345                        "OntologyTerm",
1346                        "Item"
1347                    ],
1348                    "status": "preview",
1349                    "summary": "cerebellar cortex",
1350                    "term_name": "cerebellar cortex"
1351                },
1352                {
1353                    "@id": "/sample-terms/UBERON_0002740/",
1354                    "@type": [
1355                        "SampleTerm",
1356                        "OntologyTerm",
1357                        "Item"
1358                    ],
1359                    "status": "preview",
1360                    "summary": "posterior cingulate gyrus",
1361                    "term_name": "posterior cingulate gyrus"
1362                },
1363                {
1364                    "@id": "/sample-terms/UBERON_0002771/",
1365                    "@type": [
1366                        "SampleTerm",
1367                        "OntologyTerm",
1368                        "Item"
1369                    ],
1370                    "status": "preview",
1371                    "summary": "middle temporal gyrus",
1372                    "term_name": "middle temporal gyrus"
1373                }
1374            ],
1375            "status": "preview",
1376            "summary": "multiplexed sample: Homo sapiens (male, 53 years) middle temporal gyrus tissue; Homo sapiens (male, 75 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy; ... and 14 more samples",
1377            "taxa": "Homo sapiens",
1378            "treatments": []
1379        }
1380    ],
1381    "schema_version": "26",
1382    "status": "preview",
1383    "submitted_by": {
1384        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1385        "title": "Ryan Corces"
1386    },
1387    "submitted_files_timestamp": "2025-03-20T17:55:04.389807+00:00",
1388    "summary": "single-nucleus ATAC-seq (10x multiome)",
1389    "uuid": "e3ff4f01-e62d-474a-b2d2-7e201bf225de"
1390}