IGVFDS7453IBHQ

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11        "igvf:corces_measurementSet_RP021_G3_ATAC"
12    ],
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16            "chromatin accessibility"
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18        "status": "released",
19        "term_name": "single-nucleus ATAC-seq"
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697            {
698                "category": "missing sequence specification",
699                "detail": "Measurement set [IGVFDS7453IBHQ](/measurement-sets/IGVFDS7453IBHQ/) has sequence file(s): [IGVFFI7818ZYCL](/sequence-files/IGVFFI7818ZYCL/), [IGVFFI9203SOGU](/sequence-files/IGVFFI9203SOGU/), [IGVFFI0960YHBC](/sequence-files/IGVFFI0960YHBC/), [IGVFFI3020LBOD](/sequence-files/IGVFFI3020LBOD/), [IGVFFI7242PYUG](/sequence-files/IGVFFI7242PYUG/), [IGVFFI5791HRZX](/sequence-files/IGVFFI5791HRZX/), [IGVFFI7082WEQN](/sequence-files/IGVFFI7082WEQN/), [IGVFFI4367FJBC](/sequence-files/IGVFFI4367FJBC/), [IGVFFI8524GFXE](/sequence-files/IGVFFI8524GFXE/), [IGVFFI1310CYNN](/sequence-files/IGVFFI1310CYNN/), [IGVFFI6539AFGZ](/sequence-files/IGVFFI6539AFGZ/), [IGVFFI2559VSZB](/sequence-files/IGVFFI2559VSZB/), [IGVFFI0505FZZQ](/sequence-files/IGVFFI0505FZZQ/), [IGVFFI6047SPQQ](/sequence-files/IGVFFI6047SPQQ/), [IGVFFI6315GLKK](/sequence-files/IGVFFI6315GLKK/), [IGVFFI3441RABD](/sequence-files/IGVFFI3441RABD/) 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.",
700                "level": 50,
701                "level_name": "NOT_COMPLIANT",
702                "name": "audit_missing_seqspec",
703                "path": "/measurement-sets/IGVFDS7453IBHQ/"
704            },
705            {
706                "category": "missing strand specificity",
707                "detail": "Measurement set [IGVFDS7453IBHQ](/measurement-sets/IGVFDS7453IBHQ/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
708                "level": 50,
709                "level_name": "NOT_COMPLIANT",
710                "name": "audit_missing_strand_specificity",
711                "path": "/measurement-sets/IGVFDS7453IBHQ/"
712            }
713        ],
714        "WARNING": [
715            {
716                "category": "missing analysis",
717                "detail": "Measurement set [IGVFDS7453IBHQ](/measurement-sets/IGVFDS7453IBHQ/) 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.",
718                "level": 40,
719                "level_name": "WARNING",
720                "name": "audit_input_for",
721                "path": "/measurement-sets/IGVFDS7453IBHQ/"
722            }
723        ]
724    },
725    "award": {
726        "@id": "/awards/HG012076/",
727        "component": "mapping",
728        "contact_pi": {
729            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
730            "title": "Ansuman Satpathy"
731        },
732        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
733    },
734    "control_for": [],
735    "controlled_access": false,
736    "creation_timestamp": "2025-03-19T19:55:55.717982+00:00",
737    "data_use_limitation_summaries": [
738        "No limitations"
739    ],
740    "donors": [
741        {
742            "@id": "/human-donors/IGVFDO3317CNEB/",
743            "accession": "IGVFDO3317CNEB",
744            "aliases": [
745                "igvf:corces_donor_BANN1902"
746            ],
747            "sex": "male",
748            "status": "preview",
749            "taxa": "Homo sapiens"
750        },
751        {
752            "@id": "/human-donors/IGVFDO3795BUZW/",
753            "accession": "IGVFDO3795BUZW",
754            "aliases": [
755                "igvf:corces_donor_BANN1311"
756            ],
757            "sex": "male",
758            "status": "preview",
759            "taxa": "Homo sapiens"
760        },
761        {
762            "@id": "/human-donors/IGVFDO8046LKFZ/",
763            "accession": "IGVFDO8046LKFZ",
764            "aliases": [
765                "igvf:corces_donor_BANN1242"
766            ],
767            "sex": "male",
768            "status": "preview",
769            "taxa": "Homo sapiens"
770        },
771        {
772            "@id": "/human-donors/IGVFDO7095OCLJ/",
773            "accession": "IGVFDO7095OCLJ",
774            "aliases": [
775                "igvf:corces_donor_BANN9917"
776            ],
777            "sex": "female",
778            "status": "preview",
779            "taxa": "Homo sapiens"
780        },
781        {
782            "@id": "/human-donors/IGVFDO9236YUAT/",
783            "accession": "IGVFDO9236YUAT",
784            "aliases": [
785                "igvf:corces_donor_BANN0227"
786            ],
787            "sex": "male",
788            "status": "preview",
789            "taxa": "Homo sapiens"
790        },
791        {
792            "@id": "/human-donors/IGVFDO0877AIRF/",
793            "accession": "IGVFDO0877AIRF",
794            "aliases": [
795                "igvf:corces_donor_BANN0417"
796            ],
797            "sex": "male",
798            "status": "preview",
799            "taxa": "Homo sapiens"
800        },
801        {
802            "@id": "/human-donors/IGVFDO6013FYCW/",
803            "accession": "IGVFDO6013FYCW",
804            "aliases": [
805                "igvf:corces_donor_BANN0912"
806            ],
807            "sex": "male",
808            "status": "preview",
809            "taxa": "Homo sapiens"
810        },
811        {
812            "@id": "/human-donors/IGVFDO2045AFUW/",
813            "accession": "IGVFDO2045AFUW",
814            "aliases": [
815                "igvf:corces_donor_BANN1404"
816            ],
817            "sex": "male",
818            "status": "preview",
819            "taxa": "Homo sapiens"
820        },
821        {
822            "@id": "/human-donors/IGVFDO8547HLIG/",
823            "accession": "IGVFDO8547HLIG",
824            "aliases": [
825                "igvf:corces_donor_BANN1812"
826            ],
827            "sex": "female",
828            "status": "preview",
829            "taxa": "Homo sapiens"
830        },
831        {
832            "@id": "/human-donors/IGVFDO0180JQCL/",
833            "accession": "IGVFDO0180JQCL",
834            "aliases": [
835                "igvf:corces_donor_BANN1344"
836            ],
837            "sex": "female",
838            "status": "preview",
839            "taxa": "Homo sapiens"
840        },
841        {
842            "@id": "/human-donors/IGVFDO9247BEUS/",
843            "accession": "IGVFDO9247BEUS",
844            "aliases": [
845                "igvf:corces_donor_BANN2149"
846            ],
847            "sex": "male",
848            "status": "preview",
849            "taxa": "Homo sapiens"
850        },
851        {
852            "@id": "/human-donors/IGVFDO6489DOPG/",
853            "accession": "IGVFDO6489DOPG",
854            "aliases": [
855                "igvf:corces_donor_BANN2118"
856            ],
857            "sex": "female",
858            "status": "preview",
859            "taxa": "Homo sapiens"
860        },
861        {
862            "@id": "/human-donors/IGVFDO2848YHMH/",
863            "accession": "IGVFDO2848YHMH",
864            "aliases": [
865                "igvf:corces_donor_BANN2038"
866            ],
867            "sex": "male",
868            "status": "preview",
869            "taxa": "Homo sapiens"
870        },
871        {
872            "@id": "/human-donors/IGVFDO6316TGCK/",
873            "accession": "IGVFDO6316TGCK",
874            "aliases": [
875                "igvf:corces_donor_BANN1814"
876            ],
877            "sex": "male",
878            "status": "preview",
879            "taxa": "Homo sapiens"
880        },
881        {
882            "@id": "/human-donors/IGVFDO4438WASY/",
883            "accession": "IGVFDO4438WASY",
884            "aliases": [
885                "igvf:corces_donor_BANN1644"
886            ],
887            "sex": "male",
888            "status": "preview",
889            "taxa": "Homo sapiens"
890        },
891        {
892            "@id": "/human-donors/IGVFDO4783EEYU/",
893            "accession": "IGVFDO4783EEYU",
894            "aliases": [
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896            ],
897            "sex": "male",
898            "status": "preview",
899            "taxa": "Homo sapiens"
900        }
901    ],
902    "externally_hosted": false,
903    "file_set_type": "experimental data",
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970        },
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978            "controlled_access": false,
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1080        },
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1101            "upload_status": "validated"
1102        },
1103        {
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1124        },
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1128            "aliases": [
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1146        },
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1149            "accession": "IGVFFI2559VSZB",
1150            "aliases": [
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1256        }
1257    ],
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1259    "lab": {
1260        "@id": "/labs/ryan-corces/",
1261        "title": "Ryan Corces, Gladstone Institute UCSF"
1262    },
1263    "multiome_size": 2,
1264    "onlist_files": [
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1266    ],
1267    "onlist_method": "no combination",
1268    "preferred_assay_title": "10x multiome",
1269    "protocols": [
1270        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1271    ],
1272    "related_multiome_datasets": [
1273        {
1274            "@id": "/measurement-sets/IGVFDS0829QLBI/",
1275            "accession": "IGVFDS0829QLBI",
1276            "status": "preview"
1277        }
1278    ],
1279    "samples": [
1280        {
1281            "@id": "/multiplexed-samples/IGVFSM8178OHJY/",
1282            "@type": [
1283                "MultiplexedSample",
1284                "Sample",
1285                "Item"
1286            ],
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1288            "aliases": [
1289                "igvf:corces_multiplexedSample_RP021_G3"
1290            ],
1291            "classifications": [
1292                "tissue",
1293                "multiplexed sample"
1294            ],
1295            "disease_terms": [
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1298                    "status": "in progress",
1299                    "term_name": "mild cognitive impairment"
1300                },
1301                {
1302                    "@id": "/phenotype-terms/DOID_14330/",
1303                    "status": "in progress",
1304                    "term_name": "Parkinson's disease"
1305                },
1306                {
1307                    "@id": "/phenotype-terms/DOID_9246/",
1308                    "status": "in progress",
1309                    "term_name": "cerebral amyloid angiopathy"
1310                }
1311            ],
1312            "institutional_certificates": [
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1315                    "certificate_identifier": "IP115-05",
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1317                    "status": "in progress"
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1323                    "@id": "/sample-terms/UBERON_0001874/",
1324                    "@type": [
1325                        "SampleTerm",
1326                        "OntologyTerm",
1327                        "Item"
1328                    ],
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1332                },
1333                {
1334                    "@id": "/sample-terms/UBERON_0002038/",
1335                    "@type": [
1336                        "SampleTerm",
1337                        "OntologyTerm",
1338                        "Item"
1339                    ],
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1342                    "term_name": "substantia nigra"
1343                },
1344                {
1345                    "@id": "/sample-terms/UBERON_0002740/",
1346                    "@type": [
1347                        "SampleTerm",
1348                        "OntologyTerm",
1349                        "Item"
1350                    ],
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1354                },
1355                {
1356                    "@id": "/sample-terms/UBERON_0002771/",
1357                    "@type": [
1358                        "SampleTerm",
1359                        "OntologyTerm",
1360                        "Item"
1361                    ],
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1364                    "term_name": "middle temporal gyrus"
1365                }
1366            ],
1367            "status": "preview",
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1369            "taxa": "Homo sapiens",
1370            "treatments": []
1371        }
1372    ],
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1375    "submitted_by": {
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1377        "title": "Ryan Corces"
1378    },
1379    "submitted_files_timestamp": "2025-03-20T22:05:00.143493+00:00",
1380    "summary": "single-nucleus ATAC-seq (10x multiome)",
1381    "uuid": "94bdb87d-1efc-4f86-a103-d492b7d2061e"
1382}