IGVFDS6041FJHB

1{
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11        "igvf:corces_measurementSet_RP014_G7_ATAC"
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15        "assay_slims": [
16            "chromatin accessibility"
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18        "status": "released",
19        "term_name": "single-nucleus ATAC-seq"
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689            {
690                "category": "missing sequence specification",
691                "detail": "Measurement set [IGVFDS6041FJHB](/measurement-sets/IGVFDS6041FJHB/) has sequence file(s): [IGVFFI9410XXJX](/sequence-files/IGVFFI9410XXJX/), [IGVFFI3745VBPA](/sequence-files/IGVFFI3745VBPA/), [IGVFFI4668KJPA](/sequence-files/IGVFFI4668KJPA/), [IGVFFI7757ODRI](/sequence-files/IGVFFI7757ODRI/), [IGVFFI3518YVOY](/sequence-files/IGVFFI3518YVOY/), [IGVFFI0539WXHD](/sequence-files/IGVFFI0539WXHD/), [IGVFFI8477UOPQ](/sequence-files/IGVFFI8477UOPQ/), [IGVFFI4680SBAE](/sequence-files/IGVFFI4680SBAE/), [IGVFFI0569FZUN](/sequence-files/IGVFFI0569FZUN/), [IGVFFI1930INWB](/sequence-files/IGVFFI1930INWB/), [IGVFFI3915AORT](/sequence-files/IGVFFI3915AORT/), [IGVFFI2161NNDY](/sequence-files/IGVFFI2161NNDY/), [IGVFFI9151SBEF](/sequence-files/IGVFFI9151SBEF/), [IGVFFI1729IIKB](/sequence-files/IGVFFI1729IIKB/), [IGVFFI9589TCUA](/sequence-files/IGVFFI9589TCUA/), [IGVFFI3647HPHA](/sequence-files/IGVFFI3647HPHA/) 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/IGVFDS6041FJHB/"
696            },
697            {
698                "category": "missing strand specificity",
699                "detail": "Measurement set [IGVFDS6041FJHB](/measurement-sets/IGVFDS6041FJHB/) 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/IGVFDS6041FJHB/"
704            }
705        ],
706        "WARNING": [
707            {
708                "category": "missing analysis",
709                "detail": "Measurement set [IGVFDS6041FJHB](/measurement-sets/IGVFDS6041FJHB/) 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/IGVFDS6041FJHB/"
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": "2025-03-19T19:54:49.158637+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/IGVFDO0411QFOF/",
745            "accession": "IGVFDO0411QFOF",
746            "aliases": [
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748            ],
749            "sex": "male",
750            "status": "preview",
751            "taxa": "Homo sapiens"
752        },
753        {
754            "@id": "/human-donors/IGVFDO8458OKEW/",
755            "accession": "IGVFDO8458OKEW",
756            "aliases": [
757                "igvf:corces_donor_BANN1623"
758            ],
759            "sex": "male",
760            "status": "preview",
761            "taxa": "Homo sapiens"
762        },
763        {
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765            "accession": "IGVFDO7606UOXI",
766            "aliases": [
767                "igvf:corces_donor_BANN1570"
768            ],
769            "sex": "male",
770            "status": "preview",
771            "taxa": "Homo sapiens"
772        },
773        {
774            "@id": "/human-donors/IGVFDO1302YEPX/",
775            "accession": "IGVFDO1302YEPX",
776            "aliases": [
777                "igvf:corces_donor_BANN0215"
778            ],
779            "sex": "female",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
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785            "accession": "IGVFDO0966KXTA",
786            "aliases": [
787                "igvf:corces_donor_BANN0138"
788            ],
789            "sex": "female",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
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795            "accession": "IGVFDO4783EEYU",
796            "aliases": [
797                "igvf:corces_donor_BANN1865"
798            ],
799            "sex": "male",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
804            "@id": "/human-donors/IGVFDO7732SCUF/",
805            "accession": "IGVFDO7732SCUF",
806            "aliases": [
807                "igvf:corces_donor_BANN0351"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
814            "@id": "/human-donors/IGVFDO0565OSFT/",
815            "accession": "IGVFDO0565OSFT",
816            "aliases": [
817                "igvf:corces_donor_BANN1805"
818            ],
819            "sex": "male",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
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825            "accession": "IGVFDO4191KJBR",
826            "aliases": [
827                "igvf:corces_donor_BANN0129"
828            ],
829            "sex": "male",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
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835            "accession": "IGVFDO3911JQLE",
836            "aliases": [
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838            ],
839            "sex": "male",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
844            "@id": "/human-donors/IGVFDO4015EJFT/",
845            "accession": "IGVFDO4015EJFT",
846            "aliases": [
847                "igvf:corces_donor_BANN0526"
848            ],
849            "sex": "male",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO9211DWXZ/",
855            "accession": "IGVFDO9211DWXZ",
856            "aliases": [
857                "igvf:corces_donor_BANN1352"
858            ],
859            "sex": "female",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
864            "@id": "/human-donors/IGVFDO7678VYKP/",
865            "accession": "IGVFDO7678VYKP",
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": "IGVFDO7306YMGC",
876            "aliases": [
877                "igvf:corces_donor_BANN0517"
878            ],
879            "sex": "female",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO4273OHGB/",
885            "accession": "IGVFDO4273OHGB",
886            "aliases": [
887                "igvf:corces_donor_BANN0322"
888            ],
889            "sex": "female",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        }
893    ],
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1080        },
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1103        },
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1126        },
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1129            "accession": "IGVFFI3915AORT",
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1214            },
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1222            "aliases": [
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1236                "term_name": "Illumina NovaSeq X"
1237            },
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1239            "submitted_file_name": "Multiome_ATAC_RP014_G7_L007_P061_S15_L004_I1_001.fastq.gz",
1240            "upload_status": "validated"
1241        },
1242        {
1243            "@id": "/sequence-files/IGVFFI3647HPHA/",
1244            "accession": "IGVFFI3647HPHA",
1245            "aliases": [
1246                "igvf:corces_sequenceFile_ATAC_RP014_G7_P061_L004_R1"
1247            ],
1248            "content_type": "reads",
1249            "controlled_access": false,
1250            "creation_timestamp": "2025-03-20T20:33:42.549999+00:00",
1251            "file_format": "fastq",
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1254            "md5sum": "74976826536ecc66608a4712f2c973c3",
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1256            "sequencing_platform": {
1257                "@id": "/platform-terms/EFO_0022840/",
1258                "status": "released",
1259                "term_name": "Illumina NovaSeq X"
1260            },
1261            "status": "preview",
1262            "submitted_file_name": "Multiome_ATAC_RP014_G7_L007_P061_S15_L004_R1_001.fastq.gz",
1263            "upload_status": "validated"
1264        }
1265    ],
1266    "input_for": [],
1267    "lab": {
1268        "@id": "/labs/ryan-corces/",
1269        "title": "Ryan Corces, Gladstone Institute UCSF"
1270    },
1271    "multiome_size": 2,
1272    "onlist_files": [
1273        "/tabular-files/IGVFFI7587TJLC/"
1274    ],
1275    "onlist_method": "no combination",
1276    "preferred_assay_title": "10x multiome",
1277    "protocols": [
1278        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1279    ],
1280    "related_multiome_datasets": [
1281        {
1282            "@id": "/measurement-sets/IGVFDS2731RLBA/",
1283            "accession": "IGVFDS2731RLBA",
1284            "status": "preview"
1285        }
1286    ],
1287    "samples": [
1288        {
1289            "@id": "/multiplexed-samples/IGVFSM0496VQZI/",
1290            "@type": [
1291                "MultiplexedSample",
1292                "Sample",
1293                "Item"
1294            ],
1295            "accession": "IGVFSM0496VQZI",
1296            "aliases": [
1297                "igvf:corces_multiplexedSample_RP014_G7"
1298            ],
1299            "classifications": [
1300                "tissue",
1301                "multiplexed sample"
1302            ],
1303            "disease_terms": [
1304                {
1305                    "@id": "/phenotype-terms/DOID_0080832/",
1306                    "status": "in progress",
1307                    "term_name": "mild cognitive impairment"
1308                },
1309                {
1310                    "@id": "/phenotype-terms/DOID_14330/",
1311                    "status": "in progress",
1312                    "term_name": "Parkinson's disease"
1313                },
1314                {
1315                    "@id": "/phenotype-terms/DOID_9246/",
1316                    "status": "in progress",
1317                    "term_name": "cerebral amyloid angiopathy"
1318                },
1319                {
1320                    "@id": "/phenotype-terms/MONDO_0004975/",
1321                    "status": "released",
1322                    "term_name": "Alzheimer disease"
1323                }
1324            ],
1325            "institutional_certificates": [
1326                {
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1328                    "certificate_identifier": "IP115-05",
1329                    "controlled_access": false,
1330                    "status": "in progress"
1331                }
1332            ],
1333            "modifications": [],
1334            "sample_terms": [
1335                {
1336                    "@id": "/sample-terms/UBERON_0001874/",
1337                    "@type": [
1338                        "SampleTerm",
1339                        "OntologyTerm",
1340                        "Item"
1341                    ],
1342                    "status": "preview",
1343                    "summary": "putamen",
1344                    "term_name": "putamen"
1345                },
1346                {
1347                    "@id": "/sample-terms/UBERON_0002038/",
1348                    "@type": [
1349                        "SampleTerm",
1350                        "OntologyTerm",
1351                        "Item"
1352                    ],
1353                    "status": "preview",
1354                    "summary": "substantia nigra",
1355                    "term_name": "substantia nigra"
1356                },
1357                {
1358                    "@id": "/sample-terms/UBERON_0002740/",
1359                    "@type": [
1360                        "SampleTerm",
1361                        "OntologyTerm",
1362                        "Item"
1363                    ],
1364                    "status": "preview",
1365                    "summary": "posterior cingulate gyrus",
1366                    "term_name": "posterior cingulate gyrus"
1367                },
1368                {
1369                    "@id": "/sample-terms/UBERON_0002771/",
1370                    "@type": [
1371                        "SampleTerm",
1372                        "OntologyTerm",
1373                        "Item"
1374                    ],
1375                    "status": "preview",
1376                    "summary": "middle temporal gyrus",
1377                    "term_name": "middle temporal gyrus"
1378                }
1379            ],
1380            "status": "preview",
1381            "summary": "multiplexed sample: Homo sapiens (male, 83 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (female, 78 years) middle temporal gyrus tissue associated with Parkinson's disease; ... and 14 more samples",
1382            "taxa": "Homo sapiens",
1383            "treatments": []
1384        }
1385    ],
1386    "schema_version": "26",
1387    "status": "preview",
1388    "submitted_by": {
1389        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1390        "title": "Ryan Corces"
1391    },
1392    "submitted_files_timestamp": "2025-03-20T20:33:01.554268+00:00",
1393    "summary": "single-nucleus ATAC-seq (10x multiome)",
1394    "uuid": "388aadb8-0dd3-4978-8d8c-a6294ab8b31b"
1395}