IGVFDS2066AADV

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS2066AADV/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS2066AADV",
10    "aliases": [
11        "igvf:corces_measurementSet_RP022_G4_ATAC"
12    ],
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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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703            {
704                "category": "mismatched status",
705                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [894b8828-e989-4019-811a-f7d4fde1ec70](/phenotypic-features/894b8828-e989-4019-811a-f7d4fde1ec70/).",
706                "level": 30,
707                "level_name": "INTERNAL_ACTION",
708                "name": "audit_item_status",
709                "path": "/human-donors/IGVFDO2045AFUW/"
710            },
711            {
712                "category": "mismatched status",
713                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [c1a58f29-abf8-4622-8885-66a6a187bb34](/phenotypic-features/c1a58f29-abf8-4622-8885-66a6a187bb34/).",
714                "level": 30,
715                "level_name": "INTERNAL_ACTION",
716                "name": "audit_item_status",
717                "path": "/human-donors/IGVFDO2045AFUW/"
718            },
719            {
720                "category": "mismatched status",
721                "detail": "Preview human donor [IGVFDO2045AFUW](/human-donors/IGVFDO2045AFUW/) has in progress subobject phenotypic feature [f09ab874-d34c-4112-a29b-df214539e6d3](/phenotypic-features/f09ab874-d34c-4112-a29b-df214539e6d3/).",
722                "level": 30,
723                "level_name": "INTERNAL_ACTION",
724                "name": "audit_item_status",
725                "path": "/human-donors/IGVFDO2045AFUW/"
726            }
727        ],
728        "NOT_COMPLIANT": [
729            {
730                "category": "missing sequence specification",
731                "detail": "Measurement set [IGVFDS2066AADV](/measurement-sets/IGVFDS2066AADV/) has sequence file(s): [IGVFFI4644HHEC](/sequence-files/IGVFFI4644HHEC/), [IGVFFI1803NEFZ](/sequence-files/IGVFFI1803NEFZ/), [IGVFFI6693ISNR](/sequence-files/IGVFFI6693ISNR/), [IGVFFI0669UVUE](/sequence-files/IGVFFI0669UVUE/), [IGVFFI3300JHYI](/sequence-files/IGVFFI3300JHYI/), [IGVFFI8040SYYL](/sequence-files/IGVFFI8040SYYL/), [IGVFFI8776CFLH](/sequence-files/IGVFFI8776CFLH/), [IGVFFI9252ZMSY](/sequence-files/IGVFFI9252ZMSY/), [IGVFFI0981QAKY](/sequence-files/IGVFFI0981QAKY/), [IGVFFI9747HRXH](/sequence-files/IGVFFI9747HRXH/), [IGVFFI4753IHEP](/sequence-files/IGVFFI4753IHEP/), [IGVFFI8297TUJI](/sequence-files/IGVFFI8297TUJI/), [IGVFFI8860AGQV](/sequence-files/IGVFFI8860AGQV/), [IGVFFI4628JRVD](/sequence-files/IGVFFI4628JRVD/), [IGVFFI2132JANV](/sequence-files/IGVFFI2132JANV/), [IGVFFI4501ABVK](/sequence-files/IGVFFI4501ABVK/) 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.",
732                "level": 50,
733                "level_name": "NOT_COMPLIANT",
734                "name": "audit_missing_seqspec",
735                "path": "/measurement-sets/IGVFDS2066AADV/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS2066AADV](/measurement-sets/IGVFDS2066AADV/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
740                "level": 50,
741                "level_name": "NOT_COMPLIANT",
742                "name": "audit_missing_strand_specificity",
743                "path": "/measurement-sets/IGVFDS2066AADV/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS2066AADV](/measurement-sets/IGVFDS2066AADV/) 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.",
750                "level": 40,
751                "level_name": "WARNING",
752                "name": "audit_input_for",
753                "path": "/measurement-sets/IGVFDS2066AADV/"
754            }
755        ]
756    },
757    "award": {
758        "@id": "/awards/HG012076/",
759        "component": "mapping",
760        "contact_pi": {
761            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
762            "title": "Ansuman Satpathy"
763        },
764        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
765    },
766    "control_for": [],
767    "controlled_access": false,
768    "creation_timestamp": "2025-03-19T19:56:09.955453+00:00",
769    "data_use_limitation_summaries": [
770        "No limitations"
771    ],
772    "donors": [
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774            "@id": "/human-donors/IGVFDO8670MHXE/",
775            "accession": "IGVFDO8670MHXE",
776            "aliases": [
777                "igvf:corces_donor_BANN0874"
778            ],
779            "sex": "female",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
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785            "accession": "IGVFDO2848YHMH",
786            "aliases": [
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788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO5194SXHC/",
795            "accession": "IGVFDO5194SXHC",
796            "aliases": [
797                "igvf:corces_donor_BANN1747"
798            ],
799            "sex": "male",
800            "status": "preview",
801            "taxa": "Homo sapiens"
802        },
803        {
804            "@id": "/human-donors/IGVFDO4783EEYU/",
805            "accession": "IGVFDO4783EEYU",
806            "aliases": [
807                "igvf:corces_donor_BANN1865"
808            ],
809            "sex": "male",
810            "status": "preview",
811            "taxa": "Homo sapiens"
812        },
813        {
814            "@id": "/human-donors/IGVFDO4825ZGIS/",
815            "accession": "IGVFDO4825ZGIS",
816            "aliases": [
817                "igvf:corces_donor_BANN2057"
818            ],
819            "sex": "male",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
824            "@id": "/human-donors/IGVFDO7186XJLL/",
825            "accession": "IGVFDO7186XJLL",
826            "aliases": [
827                "igvf:corces_donor_BANN1639"
828            ],
829            "sex": "male",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
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835            "accession": "IGVFDO0909BNTN",
836            "aliases": [
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838            ],
839            "sex": "male",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
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845            "accession": "IGVFDO8584FBOT",
846            "aliases": [
847                "igvf:corces_donor_BANN0315"
848            ],
849            "sex": "male",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO9236YUAT/",
855            "accession": "IGVFDO9236YUAT",
856            "aliases": [
857                "igvf:corces_donor_BANN0227"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
864            "@id": "/human-donors/IGVFDO9299YLNH/",
865            "accession": "IGVFDO9299YLNH",
866            "aliases": [
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868            ],
869            "sex": "male",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
874            "@id": "/human-donors/IGVFDO9211DWXZ/",
875            "accession": "IGVFDO9211DWXZ",
876            "aliases": [
877                "igvf:corces_donor_BANN1352"
878            ],
879            "sex": "female",
880            "status": "preview",
881            "taxa": "Homo sapiens"
882        },
883        {
884            "@id": "/human-donors/IGVFDO4103FHPT/",
885            "accession": "IGVFDO4103FHPT",
886            "aliases": [
887                "igvf:corces_donor_BANN9702"
888            ],
889            "sex": "male",
890            "status": "preview",
891            "taxa": "Homo sapiens"
892        },
893        {
894            "@id": "/human-donors/IGVFDO0967LMSM/",
895            "accession": "IGVFDO0967LMSM",
896            "aliases": [
897                "igvf:corces_donor_BANN1973"
898            ],
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900            "status": "preview",
901            "taxa": "Homo sapiens"
902        },
903        {
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906            "aliases": [
907                "igvf:corces_donor_BANN1404"
908            ],
909            "sex": "male",
910            "status": "preview",
911            "taxa": "Homo sapiens"
912        },
913        {
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915            "accession": "IGVFDO4812DEVH",
916            "aliases": [
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918            ],
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920            "status": "preview",
921            "taxa": "Homo sapiens"
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923        {
924            "@id": "/human-donors/IGVFDO9462VNBA/",
925            "accession": "IGVFDO9462VNBA",
926            "aliases": [
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928            ],
929            "sex": "male",
930            "status": "preview",
931            "taxa": "Homo sapiens"
932        }
933    ],
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940            "aliases": [
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953                "term_name": "Illumina NovaSeq X"
954            },
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957            "upload_status": "validated"
958        },
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967            "creation_timestamp": "2025-03-20T22:11:18.052108+00:00",
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978            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L002_R1_001.fastq.gz",
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980        },
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987            "content_type": "reads",
988            "controlled_access": false,
989            "creation_timestamp": "2025-03-20T22:11:35.817935+00:00",
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991            "file_size": 1090595319,
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994            "sequencing_platform": {
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997                "term_name": "Illumina NovaSeq X"
998            },
999            "status": "preview",
1000            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L003_R2_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
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1005            "accession": "IGVFFI0669UVUE",
1006            "aliases": [
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1009            "content_type": "reads",
1010            "controlled_access": false,
1011            "creation_timestamp": "2025-03-20T22:11:11.312289+00:00",
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1019                "term_name": "Illumina NovaSeq X"
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1021            "status": "preview",
1022            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L001_R3_001.fastq.gz",
1023            "upload_status": "validated"
1024        },
1025        {
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1027            "accession": "IGVFFI3300JHYI",
1028            "aliases": [
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1041                "term_name": "Illumina NovaSeq X"
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1044            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L003_I1_001.fastq.gz",
1045            "upload_status": "validated"
1046        },
1047        {
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1049            "accession": "IGVFFI8040SYYL",
1050            "aliases": [
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1053            "content_type": "reads",
1054            "controlled_access": false,
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1060            "sequencing_platform": {
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1063                "term_name": "Illumina NovaSeq X"
1064            },
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1068        },
1069        {
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1071            "accession": "IGVFFI8776CFLH",
1072            "aliases": [
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1082            "sequencing_platform": {
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1084                "status": "released",
1085                "term_name": "Illumina NovaSeq X"
1086            },
1087            "status": "preview",
1088            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L004_R3_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
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1093            "accession": "IGVFFI9252ZMSY",
1094            "aliases": [
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1096            ],
1097            "content_type": "reads",
1098            "controlled_access": false,
1099            "creation_timestamp": "2025-03-20T22:11:08.209323+00:00",
1100            "file_format": "fastq",
1101            "file_size": 1072662621,
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1103            "s3_uri": "s3://igvf-files/2025/03/20/054dbe57-7be6-445f-9b1f-c3b3b6e48ef1/IGVFFI9252ZMSY.fastq.gz",
1104            "sequencing_platform": {
1105                "@id": "/platform-terms/EFO_0022840/",
1106                "status": "released",
1107                "term_name": "Illumina NovaSeq X"
1108            },
1109            "status": "preview",
1110            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L001_R2_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI0981QAKY/",
1115            "accession": "IGVFFI0981QAKY",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_ATAC_RP022_G4_P067_L002_I1"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T22:11:14.903830+00:00",
1122            "file_format": "fastq",
1123            "file_size": 470910004,
1124            "href": "/sequence-files/IGVFFI0981QAKY/@@download/IGVFFI0981QAKY.fastq.gz",
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1126            "sequencing_platform": {
1127                "@id": "/platform-terms/EFO_0022840/",
1128                "status": "released",
1129                "term_name": "Illumina NovaSeq X"
1130            },
1131            "status": "preview",
1132            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L002_I1_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI9747HRXH/",
1137            "accession": "IGVFFI9747HRXH",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_ATAC_RP022_G4_P067_L002_R2"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T22:11:21.348974+00:00",
1144            "file_format": "fastq",
1145            "file_size": 1103172653,
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1148            "sequencing_platform": {
1149                "@id": "/platform-terms/EFO_0022840/",
1150                "status": "released",
1151                "term_name": "Illumina NovaSeq X"
1152            },
1153            "status": "preview",
1154            "submitted_file_name": "Multiome_ATAC_RP022_G4_L004_P067_S8_L002_R2_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI4753IHEP/",
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1266        },
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1269            "accession": "IGVFFI4501ABVK",
1270            "aliases": [
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1289    ],
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1291    "lab": {
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1293        "title": "Ryan Corces, Gladstone Institute UCSF"
1294    },
1295    "multiome_size": 2,
1296    "onlist_files": [
1297        "/tabular-files/IGVFFI7587TJLC/"
1298    ],
1299    "onlist_method": "no combination",
1300    "preferred_assay_title": "10x multiome",
1301    "protocols": [
1302        "https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
1303    ],
1304    "related_multiome_datasets": [
1305        {
1306            "@id": "/measurement-sets/IGVFDS8820POOK/",
1307            "accession": "IGVFDS8820POOK",
1308            "status": "preview"
1309        }
1310    ],
1311    "samples": [
1312        {
1313            "@id": "/multiplexed-samples/IGVFSM7770KKPO/",
1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
1319            "accession": "IGVFSM7770KKPO",
1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP022_G4"
1322            ],
1323            "classifications": [
1324                "tissue",
1325                "multiplexed sample"
1326            ],
1327            "disease_terms": [
1328                {
1329                    "@id": "/phenotype-terms/DOID_0080832/",
1330                    "status": "in progress",
1331                    "term_name": "mild cognitive impairment"
1332                },
1333                {
1334                    "@id": "/phenotype-terms/DOID_14330/",
1335                    "status": "in progress",
1336                    "term_name": "Parkinson's disease"
1337                },
1338                {
1339                    "@id": "/phenotype-terms/DOID_9246/",
1340                    "status": "in progress",
1341                    "term_name": "cerebral amyloid angiopathy"
1342                }
1343            ],
1344            "institutional_certificates": [
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1347                    "certificate_identifier": "IP115-05",
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1349                    "status": "in progress"
1350                }
1351            ],
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1353            "sample_terms": [
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1355                    "@id": "/sample-terms/UBERON_0001874/",
1356                    "@type": [
1357                        "SampleTerm",
1358                        "OntologyTerm",
1359                        "Item"
1360                    ],
1361                    "status": "preview",
1362                    "summary": "putamen",
1363                    "term_name": "putamen"
1364                },
1365                {
1366                    "@id": "/sample-terms/UBERON_0002038/",
1367                    "@type": [
1368                        "SampleTerm",
1369                        "OntologyTerm",
1370                        "Item"
1371                    ],
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1373                    "summary": "substantia nigra",
1374                    "term_name": "substantia nigra"
1375                },
1376                {
1377                    "@id": "/sample-terms/UBERON_0002129/",
1378                    "@type": [
1379                        "SampleTerm",
1380                        "OntologyTerm",
1381                        "Item"
1382                    ],
1383                    "status": "preview",
1384                    "summary": "cerebellar cortex",
1385                    "term_name": "cerebellar cortex"
1386                },
1387                {
1388                    "@id": "/sample-terms/UBERON_0002740/",
1389                    "@type": [
1390                        "SampleTerm",
1391                        "OntologyTerm",
1392                        "Item"
1393                    ],
1394                    "status": "preview",
1395                    "summary": "posterior cingulate gyrus",
1396                    "term_name": "posterior cingulate gyrus"
1397                },
1398                {
1399                    "@id": "/sample-terms/UBERON_0002771/",
1400                    "@type": [
1401                        "SampleTerm",
1402                        "OntologyTerm",
1403                        "Item"
1404                    ],
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1406                    "summary": "middle temporal gyrus",
1407                    "term_name": "middle temporal gyrus"
1408                }
1409            ],
1410            "status": "preview",
1411            "summary": "multiplexed sample: Homo sapiens (female, 79 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy; Homo sapiens (male, 78 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment; ... and 14 more samples",
1412            "taxa": "Homo sapiens",
1413            "treatments": []
1414        }
1415    ],
1416    "schema_version": "26",
1417    "status": "preview",
1418    "submitted_by": {
1419        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
1420        "title": "Ryan Corces"
1421    },
1422    "submitted_files_timestamp": "2025-03-20T22:11:00.240992+00:00",
1423    "summary": "single-nucleus ATAC-seq (10x multiome)",
1424    "uuid": "1c1475f0-7858-43c2-99f8-67cf28f5b893"
1425}