IGVFDS8584HIUA

1{
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3    "@id": "/measurement-sets/IGVFDS8584HIUA/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
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9    "accession": "IGVFDS8584HIUA",
10    "aliases": [
11        "igvf:corces_measurementSet_RP022_G5_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"
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703            {
704                "category": "mismatched status",
705                "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/).",
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 [d5751e04-de2d-45d7-87a7-92a56d3bf07a](/phenotypic-features/d5751e04-de2d-45d7-87a7-92a56d3bf07a/).",
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 [894b8828-e989-4019-811a-f7d4fde1ec70](/phenotypic-features/894b8828-e989-4019-811a-f7d4fde1ec70/).",
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 [IGVFDS8584HIUA](/measurement-sets/IGVFDS8584HIUA/) has sequence file(s): [IGVFFI9468HNPY](/sequence-files/IGVFFI9468HNPY/), [IGVFFI9789CFQD](/sequence-files/IGVFFI9789CFQD/), [IGVFFI9574FCFU](/sequence-files/IGVFFI9574FCFU/), [IGVFFI8266LRHV](/sequence-files/IGVFFI8266LRHV/), [IGVFFI4024WHSR](/sequence-files/IGVFFI4024WHSR/), [IGVFFI4133PODJ](/sequence-files/IGVFFI4133PODJ/), [IGVFFI0876GWPL](/sequence-files/IGVFFI0876GWPL/), [IGVFFI2088AOIK](/sequence-files/IGVFFI2088AOIK/), [IGVFFI2104AMWK](/sequence-files/IGVFFI2104AMWK/), [IGVFFI1675MDNW](/sequence-files/IGVFFI1675MDNW/), [IGVFFI3075PBFL](/sequence-files/IGVFFI3075PBFL/), [IGVFFI3445FWKL](/sequence-files/IGVFFI3445FWKL/), [IGVFFI3972HMSK](/sequence-files/IGVFFI3972HMSK/), [IGVFFI3112JJSA](/sequence-files/IGVFFI3112JJSA/), [IGVFFI5330BOMW](/sequence-files/IGVFFI5330BOMW/), [IGVFFI5821TTSU](/sequence-files/IGVFFI5821TTSU/) 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/IGVFDS8584HIUA/"
736            },
737            {
738                "category": "missing strand specificity",
739                "detail": "Measurement set [IGVFDS8584HIUA](/measurement-sets/IGVFDS8584HIUA/) 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/IGVFDS8584HIUA/"
744            }
745        ],
746        "WARNING": [
747            {
748                "category": "missing analysis",
749                "detail": "Measurement set [IGVFDS8584HIUA](/measurement-sets/IGVFDS8584HIUA/) 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/IGVFDS8584HIUA/"
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": "2025-03-19T19:56:12.911775+00:00",
769    "data_use_limitation_summaries": [
770        "No limitations"
771    ],
772    "donors": [
773        {
774            "@id": "/human-donors/IGVFDO4825ZGIS/",
775            "accession": "IGVFDO4825ZGIS",
776            "aliases": [
777                "igvf:corces_donor_BANN2057"
778            ],
779            "sex": "male",
780            "status": "preview",
781            "taxa": "Homo sapiens"
782        },
783        {
784            "@id": "/human-donors/IGVFDO5194SXHC/",
785            "accession": "IGVFDO5194SXHC",
786            "aliases": [
787                "igvf:corces_donor_BANN1747"
788            ],
789            "sex": "male",
790            "status": "preview",
791            "taxa": "Homo sapiens"
792        },
793        {
794            "@id": "/human-donors/IGVFDO0967LMSM/",
795            "accession": "IGVFDO0967LMSM",
796            "aliases": [
797                "igvf:corces_donor_BANN1973"
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/IGVFDO7186XJLL/",
815            "accession": "IGVFDO7186XJLL",
816            "aliases": [
817                "igvf:corces_donor_BANN1639"
818            ],
819            "sex": "male",
820            "status": "preview",
821            "taxa": "Homo sapiens"
822        },
823        {
824            "@id": "/human-donors/IGVFDO8670MHXE/",
825            "accession": "IGVFDO8670MHXE",
826            "aliases": [
827                "igvf:corces_donor_BANN0874"
828            ],
829            "sex": "female",
830            "status": "preview",
831            "taxa": "Homo sapiens"
832        },
833        {
834            "@id": "/human-donors/IGVFDO9211DWXZ/",
835            "accession": "IGVFDO9211DWXZ",
836            "aliases": [
837                "igvf:corces_donor_BANN1352"
838            ],
839            "sex": "female",
840            "status": "preview",
841            "taxa": "Homo sapiens"
842        },
843        {
844            "@id": "/human-donors/IGVFDO9236YUAT/",
845            "accession": "IGVFDO9236YUAT",
846            "aliases": [
847                "igvf:corces_donor_BANN0227"
848            ],
849            "sex": "male",
850            "status": "preview",
851            "taxa": "Homo sapiens"
852        },
853        {
854            "@id": "/human-donors/IGVFDO4812DEVH/",
855            "accession": "IGVFDO4812DEVH",
856            "aliases": [
857                "igvf:corces_donor_BANN1833"
858            ],
859            "sex": "male",
860            "status": "preview",
861            "taxa": "Homo sapiens"
862        },
863        {
864            "@id": "/human-donors/IGVFDO9462VNBA/",
865            "accession": "IGVFDO9462VNBA",
866            "aliases": [
867                "igvf:corces_donor_BANN2003"
868            ],
869            "sex": "male",
870            "status": "preview",
871            "taxa": "Homo sapiens"
872        },
873        {
874            "@id": "/human-donors/IGVFDO2848YHMH/",
875            "accession": "IGVFDO2848YHMH",
876            "aliases": [
877                "igvf:corces_donor_BANN2038"
878            ],
879            "sex": "male",
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/IGVFDO2045AFUW/",
895            "accession": "IGVFDO2045AFUW",
896            "aliases": [
897                "igvf:corces_donor_BANN1404"
898            ],
899            "sex": "male",
900            "status": "preview",
901            "taxa": "Homo sapiens"
902        },
903        {
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905            "accession": "IGVFDO0909BNTN",
906            "aliases": [
907                "igvf:corces_donor_BANN1554"
908            ],
909            "sex": "male",
910            "status": "preview",
911            "taxa": "Homo sapiens"
912        },
913        {
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915            "accession": "IGVFDO8584FBOT",
916            "aliases": [
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918            ],
919            "sex": "male",
920            "status": "preview",
921            "taxa": "Homo sapiens"
922        },
923        {
924            "@id": "/human-donors/IGVFDO9299YLNH/",
925            "accession": "IGVFDO9299YLNH",
926            "aliases": [
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928            ],
929            "sex": "male",
930            "status": "preview",
931            "taxa": "Homo sapiens"
932        }
933    ],
934    "externally_hosted": false,
935    "file_set_type": "experimental data",
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939            "accession": "IGVFFI9468HNPY",
940            "aliases": [
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943            "content_type": "reads",
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945            "creation_timestamp": "2025-03-20T22:12:13.700335+00:00",
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950            "sequencing_platform": {
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952                "status": "released",
953                "term_name": "Illumina NovaSeq X"
954            },
955            "status": "preview",
956            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L002_R1_001.fastq.gz",
957            "upload_status": "validated"
958        },
959        {
960            "@id": "/sequence-files/IGVFFI9789CFQD/",
961            "accession": "IGVFFI9789CFQD",
962            "aliases": [
963                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L003_I1"
964            ],
965            "content_type": "reads",
966            "controlled_access": false,
967            "creation_timestamp": "2025-03-20T22:12:23.945431+00:00",
968            "file_format": "fastq",
969            "file_size": 504713533,
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975                "term_name": "Illumina NovaSeq X"
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978            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L003_I1_001.fastq.gz",
979            "upload_status": "validated"
980        },
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983            "accession": "IGVFFI9574FCFU",
984            "aliases": [
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986            ],
987            "content_type": "reads",
988            "controlled_access": false,
989            "creation_timestamp": "2025-03-20T22:11:56.507477+00:00",
990            "file_format": "fastq",
991            "file_size": 496457638,
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993            "s3_uri": "s3://igvf-files/2025/03/20/929cea63-d780-4da4-a0d0-58b2644b766b/IGVFFI9574FCFU.fastq.gz",
994            "sequencing_platform": {
995                "@id": "/platform-terms/EFO_0022840/",
996                "status": "released",
997                "term_name": "Illumina NovaSeq X"
998            },
999            "status": "preview",
1000            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L001_I1_001.fastq.gz",
1001            "upload_status": "validated"
1002        },
1003        {
1004            "@id": "/sequence-files/IGVFFI8266LRHV/",
1005            "accession": "IGVFFI8266LRHV",
1006            "aliases": [
1007                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L003_R2"
1008            ],
1009            "content_type": "reads",
1010            "controlled_access": false,
1011            "creation_timestamp": "2025-03-20T22:12:32.273362+00:00",
1012            "file_format": "fastq",
1013            "file_size": 1208602512,
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1016            "sequencing_platform": {
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1018                "status": "released",
1019                "term_name": "Illumina NovaSeq X"
1020            },
1021            "status": "preview",
1022            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L003_R2_001.fastq.gz",
1023            "upload_status": "validated"
1024        },
1025        {
1026            "@id": "/sequence-files/IGVFFI4024WHSR/",
1027            "accession": "IGVFFI4024WHSR",
1028            "aliases": [
1029                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L004_R2"
1030            ],
1031            "content_type": "reads",
1032            "controlled_access": false,
1033            "creation_timestamp": "2025-03-20T22:12:45.328195+00:00",
1034            "file_format": "fastq",
1035            "file_size": 1220299199,
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1038            "sequencing_platform": {
1039                "@id": "/platform-terms/EFO_0022840/",
1040                "status": "released",
1041                "term_name": "Illumina NovaSeq X"
1042            },
1043            "status": "preview",
1044            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L004_R2_001.fastq.gz",
1045            "upload_status": "validated"
1046        },
1047        {
1048            "@id": "/sequence-files/IGVFFI4133PODJ/",
1049            "accession": "IGVFFI4133PODJ",
1050            "aliases": [
1051                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L003_R1"
1052            ],
1053            "content_type": "reads",
1054            "controlled_access": false,
1055            "creation_timestamp": "2025-03-20T22:12:27.446804+00:00",
1056            "file_format": "fastq",
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1060            "sequencing_platform": {
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1062                "status": "released",
1063                "term_name": "Illumina NovaSeq X"
1064            },
1065            "status": "preview",
1066            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L003_R1_001.fastq.gz",
1067            "upload_status": "validated"
1068        },
1069        {
1070            "@id": "/sequence-files/IGVFFI0876GWPL/",
1071            "accession": "IGVFFI0876GWPL",
1072            "aliases": [
1073                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L001_R3"
1074            ],
1075            "content_type": "reads",
1076            "controlled_access": false,
1077            "creation_timestamp": "2025-03-20T22:12:07.908240+00:00",
1078            "file_format": "fastq",
1079            "file_size": 2044946103,
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1082            "sequencing_platform": {
1083                "@id": "/platform-terms/EFO_0022840/",
1084                "status": "released",
1085                "term_name": "Illumina NovaSeq X"
1086            },
1087            "status": "preview",
1088            "submitted_file_name": "Multiome_ATAC_RP022_G5_L005_P067_S9_L001_R3_001.fastq.gz",
1089            "upload_status": "validated"
1090        },
1091        {
1092            "@id": "/sequence-files/IGVFFI2088AOIK/",
1093            "accession": "IGVFFI2088AOIK",
1094            "aliases": [
1095                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L002_I1"
1096            ],
1097            "content_type": "reads",
1098            "controlled_access": false,
1099            "creation_timestamp": "2025-03-20T22:12:10.762239+00:00",
1100            "file_format": "fastq",
1101            "file_size": 507473695,
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1103            "s3_uri": "s3://igvf-files/2025/03/20/17df1bd1-9ab5-440a-900f-1d082b362579/IGVFFI2088AOIK.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_G5_L005_P067_S9_L002_I1_001.fastq.gz",
1111            "upload_status": "validated"
1112        },
1113        {
1114            "@id": "/sequence-files/IGVFFI2104AMWK/",
1115            "accession": "IGVFFI2104AMWK",
1116            "aliases": [
1117                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L004_R1"
1118            ],
1119            "content_type": "reads",
1120            "controlled_access": false,
1121            "creation_timestamp": "2025-03-20T22:12:41.880723+00:00",
1122            "file_format": "fastq",
1123            "file_size": 2106800995,
1124            "href": "/sequence-files/IGVFFI2104AMWK/@@download/IGVFFI2104AMWK.fastq.gz",
1125            "s3_uri": "s3://igvf-files/2025/03/20/57194cb6-88bb-4110-a15f-39433b762877/IGVFFI2104AMWK.fastq.gz",
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_G5_L005_P067_S9_L004_R1_001.fastq.gz",
1133            "upload_status": "validated"
1134        },
1135        {
1136            "@id": "/sequence-files/IGVFFI1675MDNW/",
1137            "accession": "IGVFFI1675MDNW",
1138            "aliases": [
1139                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L002_R2"
1140            ],
1141            "content_type": "reads",
1142            "controlled_access": false,
1143            "creation_timestamp": "2025-03-20T22:12:17.637912+00:00",
1144            "file_format": "fastq",
1145            "file_size": 1216891401,
1146            "href": "/sequence-files/IGVFFI1675MDNW/@@download/IGVFFI1675MDNW.fastq.gz",
1147            "s3_uri": "s3://igvf-files/2025/03/20/7d15cdf3-9c69-4391-bdb1-9ce82784d157/IGVFFI1675MDNW.fastq.gz",
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_G5_L005_P067_S9_L002_R2_001.fastq.gz",
1155            "upload_status": "validated"
1156        },
1157        {
1158            "@id": "/sequence-files/IGVFFI3075PBFL/",
1159            "accession": "IGVFFI3075PBFL",
1160            "aliases": [
1161                "igvf:corces_sequenceFile_ATAC_RP022_G5_P067_L003_R3"
1162            ],
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1293        "title": "Ryan Corces, Gladstone Institute UCSF"
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1296    "onlist_files": [
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1298    ],
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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    ],
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1307            "accession": "IGVFDS2368FBSS",
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1312        {
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1314            "@type": [
1315                "MultiplexedSample",
1316                "Sample",
1317                "Item"
1318            ],
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1320            "aliases": [
1321                "igvf:corces_multiplexedSample_RP022_G5"
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1332                },
1333                {
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1337                },
1338                {
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1341                    "term_name": "cerebral amyloid angiopathy"
1342                }
1343            ],
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1356                    "@type": [
1357                        "SampleTerm",
1358                        "OntologyTerm",
1359                        "Item"
1360                    ],
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1362                    "summary": "putamen",
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1364                },
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1367                    "@type": [
1368                        "SampleTerm",
1369                        "OntologyTerm",
1370                        "Item"
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1375                },
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1378                    "@type": [
1379                        "SampleTerm",
1380                        "OntologyTerm",
1381                        "Item"
1382                    ],
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1385                    "term_name": "cerebellar cortex"
1386                },
1387                {
1388                    "@id": "/sample-terms/UBERON_0002740/",
1389                    "@type": [
1390                        "SampleTerm",
1391                        "OntologyTerm",
1392                        "Item"
1393                    ],
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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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1408                }
1409            ],
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1412            "taxa": "Homo sapiens",
1413            "treatments": []
1414        }
1415    ],
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1421    },
1422    "submitted_files_timestamp": "2025-03-20T22:11:56.507477+00:00",
1423    "summary": "single-nucleus ATAC-seq (10x multiome)",
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1425}