IGVFDS9871NUDC

1{
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3    "@id": "/measurement-sets/IGVFDS9871NUDC/",
4    "@type": [
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10    "aliases": [
11        "igvf:corces_measurementSet_RP021_G6_ATAC"
12    ],
13    "assay_term": {
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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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697            {
698                "category": "missing sequence specification",
699                "detail": "Measurement set [IGVFDS9871NUDC](/measurement-sets/IGVFDS9871NUDC/) has sequence file(s): [IGVFFI6951VEVI](/sequence-files/IGVFFI6951VEVI/), [IGVFFI9076NGFF](/sequence-files/IGVFFI9076NGFF/), [IGVFFI8501TYZM](/sequence-files/IGVFFI8501TYZM/), [IGVFFI6809PLRF](/sequence-files/IGVFFI6809PLRF/), [IGVFFI3350WGBM](/sequence-files/IGVFFI3350WGBM/), [IGVFFI4322XJVN](/sequence-files/IGVFFI4322XJVN/), [IGVFFI1796VPJR](/sequence-files/IGVFFI1796VPJR/), [IGVFFI0751KGZK](/sequence-files/IGVFFI0751KGZK/), [IGVFFI1693SBYV](/sequence-files/IGVFFI1693SBYV/), [IGVFFI3023MQHJ](/sequence-files/IGVFFI3023MQHJ/), [IGVFFI0408BJCV](/sequence-files/IGVFFI0408BJCV/), [IGVFFI3954NJWQ](/sequence-files/IGVFFI3954NJWQ/), [IGVFFI5789ZTYO](/sequence-files/IGVFFI5789ZTYO/), [IGVFFI3323BFCH](/sequence-files/IGVFFI3323BFCH/), [IGVFFI5689DFYY](/sequence-files/IGVFFI5689DFYY/), [IGVFFI9247ZCFI](/sequence-files/IGVFFI9247ZCFI/) 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/IGVFDS9871NUDC/"
704            },
705            {
706                "category": "missing strand specificity",
707                "detail": "Measurement set [IGVFDS9871NUDC](/measurement-sets/IGVFDS9871NUDC/) 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/IGVFDS9871NUDC/"
712            }
713        ],
714        "WARNING": [
715            {
716                "category": "missing analysis",
717                "detail": "Measurement set [IGVFDS9871NUDC](/measurement-sets/IGVFDS9871NUDC/) 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/IGVFDS9871NUDC/"
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": "2025-03-19T19:56:01.033300+00:00",
737    "data_use_limitation_summaries": [
738        "No limitations"
739    ],
740    "donors": [
741        {
742            "@id": "/human-donors/IGVFDO3795BUZW/",
743            "accession": "IGVFDO3795BUZW",
744            "aliases": [
745                "igvf:corces_donor_BANN1311"
746            ],
747            "sex": "male",
748            "status": "preview",
749            "taxa": "Homo sapiens"
750        },
751        {
752            "@id": "/human-donors/IGVFDO9247BEUS/",
753            "accession": "IGVFDO9247BEUS",
754            "aliases": [
755                "igvf:corces_donor_BANN2149"
756            ],
757            "sex": "male",
758            "status": "preview",
759            "taxa": "Homo sapiens"
760        },
761        {
762            "@id": "/human-donors/IGVFDO6489DOPG/",
763            "accession": "IGVFDO6489DOPG",
764            "aliases": [
765                "igvf:corces_donor_BANN2118"
766            ],
767            "sex": "female",
768            "status": "preview",
769            "taxa": "Homo sapiens"
770        },
771        {
772            "@id": "/human-donors/IGVFDO4783EEYU/",
773            "accession": "IGVFDO4783EEYU",
774            "aliases": [
775                "igvf:corces_donor_BANN1865"
776            ],
777            "sex": "male",
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/IGVFDO8046LKFZ/",
793            "accession": "IGVFDO8046LKFZ",
794            "aliases": [
795                "igvf:corces_donor_BANN1242"
796            ],
797            "sex": "male",
798            "status": "preview",
799            "taxa": "Homo sapiens"
800        },
801        {
802            "@id": "/human-donors/IGVFDO4438WASY/",
803            "accession": "IGVFDO4438WASY",
804            "aliases": [
805                "igvf:corces_donor_BANN1644"
806            ],
807            "sex": "male",
808            "status": "preview",
809            "taxa": "Homo sapiens"
810        },
811        {
812            "@id": "/human-donors/IGVFDO7095OCLJ/",
813            "accession": "IGVFDO7095OCLJ",
814            "aliases": [
815                "igvf:corces_donor_BANN9917"
816            ],
817            "sex": "female",
818            "status": "preview",
819            "taxa": "Homo sapiens"
820        },
821        {
822            "@id": "/human-donors/IGVFDO2848YHMH/",
823            "accession": "IGVFDO2848YHMH",
824            "aliases": [
825                "igvf:corces_donor_BANN2038"
826            ],
827            "sex": "male",
828            "status": "preview",
829            "taxa": "Homo sapiens"
830        },
831        {
832            "@id": "/human-donors/IGVFDO2045AFUW/",
833            "accession": "IGVFDO2045AFUW",
834            "aliases": [
835                "igvf:corces_donor_BANN1404"
836            ],
837            "sex": "male",
838            "status": "preview",
839            "taxa": "Homo sapiens"
840        },
841        {
842            "@id": "/human-donors/IGVFDO6013FYCW/",
843            "accession": "IGVFDO6013FYCW",
844            "aliases": [
845                "igvf:corces_donor_BANN0912"
846            ],
847            "sex": "male",
848            "status": "preview",
849            "taxa": "Homo sapiens"
850        },
851        {
852            "@id": "/human-donors/IGVFDO0877AIRF/",
853            "accession": "IGVFDO0877AIRF",
854            "aliases": [
855                "igvf:corces_donor_BANN0417"
856            ],
857            "sex": "male",
858            "status": "preview",
859            "taxa": "Homo sapiens"
860        },
861        {
862            "@id": "/human-donors/IGVFDO6316TGCK/",
863            "accession": "IGVFDO6316TGCK",
864            "aliases": [
865                "igvf:corces_donor_BANN1814"
866            ],
867            "sex": "male",
868            "status": "preview",
869            "taxa": "Homo sapiens"
870        },
871        {
872            "@id": "/human-donors/IGVFDO0180JQCL/",
873            "accession": "IGVFDO0180JQCL",
874            "aliases": [
875                "igvf:corces_donor_BANN1344"
876            ],
877            "sex": "female",
878            "status": "preview",
879            "taxa": "Homo sapiens"
880        },
881        {
882            "@id": "/human-donors/IGVFDO3317CNEB/",
883            "accession": "IGVFDO3317CNEB",
884            "aliases": [
885                "igvf:corces_donor_BANN1902"
886            ],
887            "sex": "male",
888            "status": "preview",
889            "taxa": "Homo sapiens"
890        },
891        {
892            "@id": "/human-donors/IGVFDO8547HLIG/",
893            "accession": "IGVFDO8547HLIG",
894            "aliases": [
895                "igvf:corces_donor_BANN1812"
896            ],
897            "sex": "female",
898            "status": "preview",
899            "taxa": "Homo sapiens"
900        }
901    ],
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929            "accession": "IGVFFI9076NGFF",
930            "aliases": [
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935            "creation_timestamp": "2025-03-20T22:07:44.762471+00:00",
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952            "aliases": [
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955            "content_type": "reads",
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970        },
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978            "controlled_access": false,
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992        },
993        {
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995            "accession": "IGVFFI3350WGBM",
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1014        },
1015        {
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1018            "aliases": [
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1080        },
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1102        },
1103        {
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1105            "accession": "IGVFFI3023MQHJ",
1106            "aliases": [
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1124        },
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1126            "@id": "/sequence-files/IGVFFI0408BJCV/",
1127            "accession": "IGVFFI0408BJCV",
1128            "aliases": [
1129                "igvf:corces_sequenceFile_ATAC_RP021_G6_P067_L001_R2"
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1144            "submitted_file_name": "Multiome_ATAC_RP021_G6_L006_P067_S4_L001_R2_001.fastq.gz",
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1146        },
1147        {
1148            "@id": "/sequence-files/IGVFFI3954NJWQ/",
1149            "accession": "IGVFFI3954NJWQ",
1150            "aliases": [
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1256        }
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1259    "lab": {
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1261        "title": "Ryan Corces, Gladstone Institute UCSF"
1262    },
1263    "multiome_size": 2,
1264    "onlist_files": [
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1266    ],
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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/IGVFDS1354SHUU/",
1275            "accession": "IGVFDS1354SHUU",
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1277        }
1278    ],
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1280        {
1281            "@id": "/multiplexed-samples/IGVFSM0125OEIT/",
1282            "@type": [
1283                "MultiplexedSample",
1284                "Sample",
1285                "Item"
1286            ],
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1288            "aliases": [
1289                "igvf:corces_multiplexedSample_RP021_G6"
1290            ],
1291            "classifications": [
1292                "tissue",
1293                "multiplexed sample"
1294            ],
1295            "disease_terms": [
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1299                    "term_name": "mild cognitive impairment"
1300                },
1301                {
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1303                    "status": "in progress",
1304                    "term_name": "Parkinson's disease"
1305                },
1306                {
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1308                    "status": "in progress",
1309                    "term_name": "cerebral amyloid angiopathy"
1310                }
1311            ],
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1324                    "@type": [
1325                        "SampleTerm",
1326                        "OntologyTerm",
1327                        "Item"
1328                    ],
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1332                },
1333                {
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1335                    "@type": [
1336                        "SampleTerm",
1337                        "OntologyTerm",
1338                        "Item"
1339                    ],
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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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1365                }
1366            ],
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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": "2025-03-20T22:07:22.068932+00:00",
1380    "summary": "single-nucleus ATAC-seq (10x multiome)",
1381    "uuid": "42735f3f-1335-405c-b654-4e43f616dc35"
1382}