IGVFDS0855IFDW

1{
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3    "@id": "/measurement-sets/IGVFDS0855IFDW/",
4    "@type": [
5        "MeasurementSet",
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7        "Item"
8    ],
9    "accession": "IGVFDS0855IFDW",
10    "aliases": [
11        "igvf:corces_measurementSet_RP012_G2_ATAC"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0002762/",
15        "assay_slims": [
16            "chromatin accessibility"
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18        "status": "released",
19        "term_name": "single-nucleus ATAC-seq"
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703            {
704                "category": "mismatched status",
705                "detail": "Preview human donor [IGVFDO7109IWDJ](/human-donors/IGVFDO7109IWDJ/) has in progress subobject phenotypic feature [5c7de610-9d77-4450-b755-6296339a9a06](/phenotypic-features/5c7de610-9d77-4450-b755-6296339a9a06/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO7109IWDJ/"
710            }
711        ],
712        "NOT_COMPLIANT": [
713            {
714                "category": "missing sequence specification",
715                "detail": "Measurement set [IGVFDS0855IFDW](/measurement-sets/IGVFDS0855IFDW/) has sequence file(s): [IGVFFI5269WVDH](/sequence-files/IGVFFI5269WVDH/), [IGVFFI1254NHVT](/sequence-files/IGVFFI1254NHVT/), [IGVFFI5106UYFY](/sequence-files/IGVFFI5106UYFY/), [IGVFFI4035VSLT](/sequence-files/IGVFFI4035VSLT/), [IGVFFI0077ROSY](/sequence-files/IGVFFI0077ROSY/), [IGVFFI7761GARN](/sequence-files/IGVFFI7761GARN/), [IGVFFI7624DIZL](/sequence-files/IGVFFI7624DIZL/), [IGVFFI8683VDXF](/sequence-files/IGVFFI8683VDXF/), [IGVFFI8986KLKJ](/sequence-files/IGVFFI8986KLKJ/), [IGVFFI8925BNDI](/sequence-files/IGVFFI8925BNDI/), [IGVFFI3662OYXL](/sequence-files/IGVFFI3662OYXL/), [IGVFFI3707ZLSK](/sequence-files/IGVFFI3707ZLSK/), [IGVFFI9080AWMP](/sequence-files/IGVFFI9080AWMP/), [IGVFFI2578PJNF](/sequence-files/IGVFFI2578PJNF/), [IGVFFI6620DWTL](/sequence-files/IGVFFI6620DWTL/), [IGVFFI6426RTJW](/sequence-files/IGVFFI6426RTJW/) 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/IGVFDS0855IFDW/"
720            },
721            {
722                "category": "missing strand specificity",
723                "detail": "Measurement set [IGVFDS0855IFDW](/measurement-sets/IGVFDS0855IFDW/) 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/IGVFDS0855IFDW/"
728            }
729        ],
730        "WARNING": [
731            {
732                "category": "missing analysis",
733                "detail": "Measurement set [IGVFDS0855IFDW](/measurement-sets/IGVFDS0855IFDW/) 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/IGVFDS0855IFDW/"
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": "2025-03-19T19:53:58.254282+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/IGVFDO6013FYCW/",
769            "accession": "IGVFDO6013FYCW",
770            "aliases": [
771                "igvf:corces_donor_BANN0912"
772            ],
773            "sex": "male",
774            "status": "preview",
775            "taxa": "Homo sapiens"
776        },
777        {
778            "@id": "/human-donors/IGVFDO1464XWYC/",
779            "accession": "IGVFDO1464XWYC",
780            "aliases": [
781                "igvf:corces_donor_BANN1809"
782            ],
783            "sex": "male",
784            "status": "preview",
785            "taxa": "Homo sapiens"
786        },
787        {
788            "@id": "/human-donors/IGVFDO1797DNPW/",
789            "accession": "IGVFDO1797DNPW",
790            "aliases": [
791                "igvf:corces_donor_BANN1827"
792            ],
793            "sex": "male",
794            "status": "preview",
795            "taxa": "Homo sapiens"
796        },
797        {
798            "@id": "/human-donors/IGVFDO4783EEYU/",
799            "accession": "IGVFDO4783EEYU",
800            "aliases": [
801                "igvf:corces_donor_BANN1865"
802            ],
803            "sex": "male",
804            "status": "preview",
805            "taxa": "Homo sapiens"
806        },
807        {
808            "@id": "/human-donors/IGVFDO7606UOXI/",
809            "accession": "IGVFDO7606UOXI",
810            "aliases": [
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812            ],
813            "sex": "male",
814            "status": "preview",
815            "taxa": "Homo sapiens"
816        },
817        {
818            "@id": "/human-donors/IGVFDO7754VJKM/",
819            "accession": "IGVFDO7754VJKM",
820            "aliases": [
821                "igvf:corces_donor_BANN0341"
822            ],
823            "sex": "male",
824            "status": "preview",
825            "taxa": "Homo sapiens"
826        },
827        {
828            "@id": "/human-donors/IGVFDO0909BNTN/",
829            "accession": "IGVFDO0909BNTN",
830            "aliases": [
831                "igvf:corces_donor_BANN1554"
832            ],
833            "sex": "male",
834            "status": "preview",
835            "taxa": "Homo sapiens"
836        },
837        {
838            "@id": "/human-donors/IGVFDO8800RKVB/",
839            "accession": "IGVFDO8800RKVB",
840            "aliases": [
841                "igvf:corces_donor_BANN1872"
842            ],
843            "sex": "female",
844            "status": "preview",
845            "taxa": "Homo sapiens"
846        },
847        {
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849            "accession": "IGVFDO5718REZU",
850            "aliases": [
851                "igvf:corces_donor_BANN9926"
852            ],
853            "sex": "female",
854            "status": "preview",
855            "taxa": "Homo sapiens"
856        },
857        {
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859            "accession": "IGVFDO7109IWDJ",
860            "aliases": [
861                "igvf:corces_donor_BANN2005"
862            ],
863            "sex": "male",
864            "status": "preview",
865            "taxa": "Homo sapiens"
866        },
867        {
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869            "accession": "IGVFDO8547HLIG",
870            "aliases": [
871                "igvf:corces_donor_BANN1812"
872            ],
873            "sex": "female",
874            "status": "preview",
875            "taxa": "Homo sapiens"
876        },
877        {
878            "@id": "/human-donors/IGVFDO5214IKNF/",
879            "accession": "IGVFDO5214IKNF",
880            "aliases": [
881                "igvf:corces_donor_BANN1070"
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        {
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899            "accession": "IGVFDO4053HEKW",
900            "aliases": [
901                "igvf:corces_donor_BANN1317"
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        }
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924            "aliases": [
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950            "controlled_access": false,
951            "creation_timestamp": "2025-03-20T20:13:43.811403+00:00",
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987        {
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989            "accession": "IGVFFI4035VSLT",
990            "aliases": [
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993            "content_type": "reads",
994            "controlled_access": false,
995            "creation_timestamp": "2025-03-20T20:13:28.366424+00:00",
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1007            "upload_status": "validated"
1008        },
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1012            "aliases": [
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1030        },
1031        {
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1033            "accession": "IGVFFI7761GARN",
1034            "aliases": [
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1037            "content_type": "reads",
1038            "controlled_access": false,
1039            "creation_timestamp": "2025-03-20T20:13:31.231459+00:00",
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1069                "term_name": "Illumina NovaSeq X"
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1072            "submitted_file_name": "Multiome_ATAC_RP012_G2_L002_P059_S82_L006_I1_001.fastq.gz",
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1074        },
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1078            "aliases": [
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1091                "term_name": "Illumina NovaSeq X"
1092            },
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1096        },
1097        {
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1099            "accession": "IGVFFI8986KLKJ",
1100            "aliases": [
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1111                "@id": "/platform-terms/EFO_0022840/",
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1113                "term_name": "Illumina NovaSeq X"
1114            },
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1116            "submitted_file_name": "Multiome_ATAC_RP012_G2_L002_P059_S82_L007_R1_001.fastq.gz",
1117            "upload_status": "validated"
1118        },
1119        {
1120            "@id": "/sequence-files/IGVFFI8925BNDI/",
1121            "accession": "IGVFFI8925BNDI",
1122            "aliases": [
1123                "igvf:corces_sequenceFile_ATAC_RP012_G2_P059_L007_R2"
1124            ],
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1126            "controlled_access": false,
1127            "creation_timestamp": "2025-03-20T20:13:57.407978+00:00",
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1135                "term_name": "Illumina NovaSeq X"
1136            },
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1138            "submitted_file_name": "Multiome_ATAC_RP012_G2_L002_P059_S82_L007_R2_001.fastq.gz",
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1140        },
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1143            "accession": "IGVFFI3662OYXL",
1144            "aliases": [
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1146            ],
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1149            "creation_timestamp": "2025-03-20T20:13:51.422013+00:00",
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1154            "sequencing_platform": {
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1157                "term_name": "Illumina NovaSeq X"
1158            },
1159            "status": "preview",
1160            "submitted_file_name": "Multiome_ATAC_RP012_G2_L002_P059_S82_L007_I1_001.fastq.gz",
1161            "upload_status": "validated"
1162        },
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1250        },
1251        {
1252            "@id": "/sequence-files/IGVFFI6426RTJW/",
1253            "accession": "IGVFFI6426RTJW",
1254            "aliases": [
1255                "igvf:corces_sequenceFile_ATAC_RP012_G2_P059_L008_R2"
1256            ],
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1273    ],
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1275    "lab": {
1276        "@id": "/labs/ryan-corces/",
1277        "title": "Ryan Corces, Gladstone Institute UCSF"
1278    },
1279    "multiome_size": 2,
1280    "onlist_files": [
1281        "/tabular-files/IGVFFI7587TJLC/"
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        {
1290            "@id": "/measurement-sets/IGVFDS1447ZIXP/",
1291            "accession": "IGVFDS1447ZIXP",
1292            "status": "preview"
1293        }
1294    ],
1295    "samples": [
1296        {
1297            "@id": "/multiplexed-samples/IGVFSM3226MLFV/",
1298            "@type": [
1299                "MultiplexedSample",
1300                "Sample",
1301                "Item"
1302            ],
1303            "accession": "IGVFSM3226MLFV",
1304            "aliases": [
1305                "igvf:corces_multiplexedSample_RP012_G2"
1306            ],
1307            "classifications": [
1308                "tissue",
1309                "multiplexed sample"
1310            ],
1311            "disease_terms": [
1312                {
1313                    "@id": "/phenotype-terms/DOID_0080832/",
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": [
1329                {
1330                    "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
1331                    "certificate_identifier": "IP115-05",
1332                    "controlled_access": false,
1333                    "status": "in progress"
1334                }
1335            ],
1336            "modifications": [],
1337            "sample_terms": [
1338                {
1339                    "@id": "/sample-terms/UBERON_0001874/",
1340                    "@type": [
1341                        "SampleTerm",
1342                        "OntologyTerm",
1343                        "Item"
1344                    ],
1345                    "status": "preview",
1346                    "summary": "putamen",
1347                    "term_name": "putamen"
1348                },
1349                {
1350                    "@id": "/sample-terms/UBERON_0002038/",
1351                    "@type": [
1352                        "SampleTerm",
1353                        "OntologyTerm",
1354                        "Item"
1355                    ],
1356                    "status": "preview",
1357                    "summary": "substantia nigra",
1358                    "term_name": "substantia nigra"
1359                },
1360                {
1361                    "@id": "/sample-terms/UBERON_0002129/",
1362                    "@type": [
1363                        "SampleTerm",
1364                        "OntologyTerm",
1365                        "Item"
1366                    ],
1367                    "status": "preview",
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                    ],
1378                    "status": "preview",
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                    ],
1389                    "status": "preview",
1390                    "summary": "middle temporal gyrus",
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    ],
1400    "schema_version": "26",
1401    "status": "preview",
1402    "submitted_by": {
1403        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1404        "title": "Ryan Corces"
1405    },
1406    "submitted_files_timestamp": "2025-03-20T20:13:22.861862+00:00",
1407    "summary": "single-nucleus ATAC-seq (10x multiome)",
1408    "uuid": "fac89f7b-eca2-4151-b87f-b16a043aac04"
1409}