IGVFDS7361KZSL

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS7361KZSL/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS7361KZSL",
10    "aliases": [
11        "ali-mortazavi:004_67H_illumina"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0003109/",
15        "assay_slims": [
16            "gene expression"
17        ],
18        "status": "released",
19        "term_name": "single-nucleus RNA sequencing assay"
20    },
21    "audit": {
22        "INTERNAL_ACTION": [
23            {
24                "category": "mismatched status",
25                "detail": "Released multiplexed sample [IGVFSM1327NHSH](/multiplexed-samples/IGVFSM1327NHSH/) has in progress subobject tabular file [IGVFFI6237SLBZ](/tabular-files/IGVFFI6237SLBZ/).",
26                "level": 30,
27                "level_name": "INTERNAL_ACTION",
28                "name": "audit_item_status",
29                "path": "/multiplexed-samples/IGVFSM1327NHSH/"
30            },
31            {
32                "category": "missing publication",
33                "detail": "Multiplexed sample [IGVFSM1327NHSH](/multiplexed-samples/IGVFSM1327NHSH/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
34                "level": 30,
35                "level_name": "INTERNAL_ACTION",
36                "name": "audit_sample_missing_publication",
37                "path": "/multiplexed-samples/IGVFSM1327NHSH/"
38            },
39            {
40                "category": "missing publication",
41                "detail": "Measurement set [IGVFDS7361KZSL](/measurement-sets/IGVFDS7361KZSL/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
42                "level": 30,
43                "level_name": "INTERNAL_ACTION",
44                "name": "audit_file_set_missing_publication",
45                "path": "/measurement-sets/IGVFDS7361KZSL/"
46            },
47            {
48                "category": "mismatched status",
49                "detail": "Released measurement set [IGVFDS7361KZSL](/measurement-sets/IGVFDS7361KZSL/) has in progress subobject tabular file [IGVFFI2591OFQO](/tabular-files/IGVFFI2591OFQO/).",
50                "level": 30,
51                "level_name": "INTERNAL_ACTION",
52                "name": "audit_item_status",
53                "path": "/measurement-sets/IGVFDS7361KZSL/"
54            },
55            {
56                "category": "mismatched status",
57                "detail": "Released measurement set [IGVFDS7361KZSL](/measurement-sets/IGVFDS7361KZSL/) has in progress subobject tabular file [IGVFFI1138MCVX](/tabular-files/IGVFFI1138MCVX/).",
58                "level": 30,
59                "level_name": "INTERNAL_ACTION",
60                "name": "audit_item_status",
61                "path": "/measurement-sets/IGVFDS7361KZSL/"
62            }
63        ]
64    },
65    "award": {
66        "@id": "/awards/HG012077/",
67        "component": "mapping",
68        "contact_pi": {
69            "@id": "/users/2c33e192-e815-4384-a220-72a0992cbe24/",
70            "title": "Ali Mortazavi"
71        },
72        "title": "Center for Mouse Genomic Variation at Single Cell Resolution"
73    },
74    "control_for": [],
75    "creation_timestamp": "2023-10-05T18:13:25.541662+00:00",
76    "data_use_limitation_summaries": [
77        "no certificate"
78    ],
79    "donors": [
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82            "accession": "IGVFDO5502NJPS",
83            "aliases": [
84                "ali-mortazavi:038_129S1J_10F"
85            ],
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87            "status": "released",
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89            "taxa": "Mus musculus"
90        },
91        {
92            "@id": "/rodent-donors/IGVFDO0681EHNP/",
93            "accession": "IGVFDO0681EHNP",
94            "aliases": [
95                "ali-mortazavi:052_NZOJ_10F"
96            ],
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98            "status": "released",
99            "strain_background": "NZO/H1LtJ (NZO)",
100            "taxa": "Mus musculus"
101        },
102        {
103            "@id": "/rodent-donors/IGVFDO0751WQHI/",
104            "accession": "IGVFDO0751WQHI",
105            "aliases": [
106                "ali-mortazavi:080_PWKJ_10F"
107            ],
108            "sex": "female",
109            "status": "released",
110            "strain_background": "PWK/PhJ (PWK)",
111            "taxa": "Mus musculus"
112        },
113        {
114            "@id": "/rodent-donors/IGVFDO2319OUEC/",
115            "accession": "IGVFDO2319OUEC",
116            "aliases": [
117                "ali-mortazavi:045_129S1J_10M"
118            ],
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120            "status": "released",
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122            "taxa": "Mus musculus"
123        },
124        {
125            "@id": "/rodent-donors/IGVFDO5539RLXJ/",
126            "accession": "IGVFDO5539RLXJ",
127            "aliases": [
128                "ali-mortazavi:029_AJ_10M"
129            ],
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133            "taxa": "Mus musculus"
134        },
135        {
136            "@id": "/rodent-donors/IGVFDO3603MEIO/",
137            "accession": "IGVFDO3603MEIO",
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139                "ali-mortazavi:084_PWKJ_10F"
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142            "status": "released",
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145        },
146        {
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148            "accession": "IGVFDO7007WBAX",
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150                "ali-mortazavi:016_B6J_10F"
151            ],
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153            "status": "released",
154            "strain_background": "C57BL/6J (B6)",
155            "taxa": "Mus musculus"
156        },
157        {
158            "@id": "/rodent-donors/IGVFDO7610XXRR/",
159            "accession": "IGVFDO7610XXRR",
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161                "ali-mortazavi:072_NODJ_10F"
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167        },
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170            "accession": "IGVFDO9202WGJZ",
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172                "ali-mortazavi:085_PWKJ_10M"
173            ],
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178        },
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181            "accession": "IGVFDO1643VEDI",
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183                "ali-mortazavi:019_B6J_10M"
184            ],
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188            "taxa": "Mus musculus"
189        },
190        {
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192            "accession": "IGVFDO6066JIEJ",
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195            ],
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200        },
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203            "accession": "IGVFDO6141KSSQ",
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206            ],
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211        },
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217            ],
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222        },
223        {
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228            ],
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231            "strain_background": "WSB/EiJ (WSB)",
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233        },
234        {
235            "@id": "/rodent-donors/IGVFDO3436ZMLY/",
236            "accession": "IGVFDO3436ZMLY",
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238                "ali-mortazavi:091_CASTJ_10M"
239            ],
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241            "status": "released",
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244        },
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247            "accession": "IGVFDO9374WXKK",
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249                "ali-mortazavi:028_AJ_10F"
250            ],
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252            "status": "released",
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255        },
256        {
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277        },
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283            ],
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288        },
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296            "status": "released",
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299        },
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309            "taxa": "Mus musculus"
310        },
311        {
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314            "aliases": [
315                "ali-mortazavi:035_AJ_10M"
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318            "status": "released",
319            "strain_background": "A/J (AJ)",
320            "taxa": "Mus musculus"
321        },
322        {
323            "@id": "/rodent-donors/IGVFDO3640WUBU/",
324            "accession": "IGVFDO3640WUBU",
325            "aliases": [
326                "ali-mortazavi:066_NODJ_10F"
327            ],
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329            "status": "released",
330            "strain_background": "NOD/ShiLtJ (NOD)",
331            "taxa": "Mus musculus"
332        },
333        {
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335            "accession": "IGVFDO9510ILZG",
336            "aliases": [
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340            "status": "released",
341            "strain_background": "NZO/H1LtJ (NZO)",
342            "taxa": "Mus musculus"
343        },
344        {
345            "@id": "/rodent-donors/IGVFDO3762EAWT/",
346            "accession": "IGVFDO3762EAWT",
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348                "ali-mortazavi:076_PWKJ_10F"
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351            "status": "released",
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353            "taxa": "Mus musculus"
354        },
355        {
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360            ],
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362            "status": "released",
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364            "taxa": "Mus musculus"
365        },
366        {
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368            "accession": "IGVFDO1477BPVO",
369            "aliases": [
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373            "status": "released",
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375            "taxa": "Mus musculus"
376        },
377        {
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380            "aliases": [
381                "ali-mortazavi:059_WSBJ_10M"
382            ],
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384            "status": "released",
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386            "taxa": "Mus musculus"
387        },
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390            "accession": "IGVFDO6219LVKW",
391            "aliases": [
392                "ali-mortazavi:032_AJ_10F"
393            ],
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398        },
399        {
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401            "accession": "IGVFDO9560CEGZ",
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406            "status": "released",
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408            "taxa": "Mus musculus"
409        },
410        {
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414                "ali-mortazavi:089_CASTJ_10M"
415            ],
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417            "status": "released",
418            "strain_background": "CAST/EiJ (CAST)",
419            "taxa": "Mus musculus"
420        },
421        {
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423            "accession": "IGVFDO5085MJSP",
424            "aliases": [
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427            "sex": "female",
428            "status": "released",
429            "strain_background": "NZO/H1LtJ (NZO)",
430            "taxa": "Mus musculus"
431        },
432        {
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434            "accession": "IGVFDO7951JDSP",
435            "aliases": [
436                "ali-mortazavi:026_AJ_10F"
437            ],
438            "sex": "female",
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440            "strain_background": "A/J (AJ)",
441            "taxa": "Mus musculus"
442        },
443        {
444            "@id": "/rodent-donors/IGVFDO2831PZHE/",
445            "accession": "IGVFDO2831PZHE",
446            "aliases": [
447                "ali-mortazavi:077_PWKJ_10M"
448            ],
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450            "status": "released",
451            "strain_background": "PWK/PhJ (PWK)",
452            "taxa": "Mus musculus"
453        },
454        {
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456            "accession": "IGVFDO0813DZTW",
457            "aliases": [
458                "ali-mortazavi:069_NODJ_10M"
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462            "strain_background": "NOD/ShiLtJ (NOD)",
463            "taxa": "Mus musculus"
464        },
465        {
466            "@id": "/rodent-donors/IGVFDO4707SGWM/",
467            "accession": "IGVFDO4707SGWM",
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469                "ali-mortazavi:051_NZOJ_10M"
470            ],
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475        },
476        {
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478            "accession": "IGVFDO7254QNQZ",
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481            ],
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486        },
487        {
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497        },
498        {
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500            "accession": "IGVFDO8152XDDC",
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503            ],
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505            "status": "released",
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507            "taxa": "Mus musculus"
508        },
509        {
510            "@id": "/rodent-donors/IGVFDO5872DFML/",
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514            ],
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518            "taxa": "Mus musculus"
519        },
520        {
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529            "taxa": "Mus musculus"
530        },
531        {
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533            "accession": "IGVFDO5523UFUN",
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538            "status": "released",
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541        },
542        {
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544            "accession": "IGVFDO4788BIQB",
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552        },
553        {
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555            "accession": "IGVFDO7255VZBN",
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557                "ali-mortazavi:062_WSBJ_10F"
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560            "status": "released",
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562            "taxa": "Mus musculus"
563        },
564        {
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566            "accession": "IGVFDO8322VYDU",
567            "aliases": [
568                "ali-mortazavi:093_CASTJ_10M"
569            ],
570            "sex": "male",
571            "status": "released",
572            "strain_background": "CAST/EiJ (CAST)",
573            "taxa": "Mus musculus"
574        },
575        {
576            "@id": "/rodent-donors/IGVFDO2292YGGE/",
577            "accession": "IGVFDO2292YGGE",
578            "aliases": [
579                "ali-mortazavi:049_NZOJ_10M"
580            ],
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583            "strain_background": "NZO/H1LtJ (NZO)",
584            "taxa": "Mus musculus"
585        },
586        {
587            "@id": "/rodent-donors/IGVFDO4725SNCJ/",
588            "accession": "IGVFDO4725SNCJ",
589            "aliases": [
590                "ali-mortazavi:017_B6J_10M"
591            ],
592            "sex": "male",
593            "status": "released",
594            "strain_background": "C57BL/6J (B6)",
595            "taxa": "Mus musculus"
596        },
597        {
598            "@id": "/rodent-donors/IGVFDO0430HQIU/",
599            "accession": "IGVFDO0430HQIU",
600            "aliases": [
601                "ali-mortazavi:041_129S1J_10M"
602            ],
603            "sex": "male",
604            "status": "released",
605            "strain_background": "129S1/SvImJ (129)",
606            "taxa": "Mus musculus"
607        },
608        {
609            "@id": "/rodent-donors/IGVFDO1744FDIX/",
610            "accession": "IGVFDO1744FDIX",
611            "aliases": [
612                "ali-mortazavi:036_129S1J_10F"
613            ],
614            "sex": "female",
615            "status": "released",
616            "strain_background": "129S1/SvImJ (129)",
617            "taxa": "Mus musculus"
618        },
619        {
620            "@id": "/rodent-donors/IGVFDO0624KKTV/",
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1172        },
1173        {
1174            "@id": "/configuration-files/IGVFFI8363DJHV/",
1175            "accession": "IGVFFI8363DJHV",
1176            "content_type": "seqspec",
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1186        {
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1189            "content_type": "seqspec",
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1196            "status": "released",
1197            "upload_status": "validated"
1198        },
1199        {
1200            "@id": "/configuration-files/IGVFFI0311XEDU/",
1201            "accession": "IGVFFI0311XEDU",
1202            "content_type": "seqspec",
1203            "creation_timestamp": "2024-09-16T17:26:25.859090+00:00",
1204            "file_format": "yaml",
1205            "file_size": 1353,
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1209            "status": "released",
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1211        }
1212    ],
1213    "input_for": [
1214        "/analysis-sets/IGVFDS1158CYSK/"
1215    ],
1216    "lab": {
1217        "@id": "/labs/ali-mortazavi/",
1218        "title": "Ali Mortazavi, UCI"
1219    },
1220    "notes": "Preferred_assay_titles enum Parse Split-seq has been renamed to be Parse SPLiT-seq.",
1221    "onlist_files": [
1222        "/tabular-files/IGVFFI2591OFQO/",
1223        "/tabular-files/IGVFFI1138MCVX/"
1224    ],
1225    "onlist_method": "multi",
1226    "preferred_assay_title": "Parse SPLiT-seq",
1227    "protocols": [
1228        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-dm6gp3zedvzp/v2",
1229        "https://www.protocols.io/view/protocol-to-isolate-and-fix-nuclei-from-flash-froz-kxygx396zg8j/v2",
1230        "https://www.protocols.io/view/evercode-wt-mega-v2-2-1-8epv5xxrng1b/v1",
1231        "https://www.protocols.io/view/evercode-single-index-pcr-5jyl82k9rl2w/v1"
1232    ],
1233    "release_timestamp": "2025-04-18T22:58:19.565102+00:00",
1234    "samples": [
1235        {
1236            "@id": "/multiplexed-samples/IGVFSM1327NHSH/",
1237            "@type": [
1238                "MultiplexedSample",
1239                "Sample",
1240                "Item"
1241            ],
1242            "accession": "IGVFSM1327NHSH",
1243            "aliases": [
1244                "ali-mortazavi:subpool_004_67H"
1245            ],
1246            "cellular_sub_pool": "004_67H",
1247            "classifications": [
1248                "tissue",
1249                "multiplexed sample"
1250            ],
1251            "disease_terms": [],
1252            "institutional_certificates": [],
1253            "modifications": [],
1254            "sample_terms": [
1255                {
1256                    "@id": "/sample-terms/UBERON_0000948/",
1257                    "@type": [
1258                        "SampleTerm",
1259                        "OntologyTerm",
1260                        "Item"
1261                    ],
1262                    "status": "released",
1263                    "summary": "heart",
1264                    "term_name": "heart"
1265                },
1266                {
1267                    "@id": "/sample-terms/UBERON_0002107/",
1268                    "@type": [
1269                        "SampleTerm",
1270                        "OntologyTerm",
1271                        "Item"
1272                    ],
1273                    "status": "released",
1274                    "summary": "liver",
1275                    "term_name": "liver"
1276                }
1277            ],
1278            "status": "released",
1279            "summary": "multiplexed sample: Mus musculus CAST/EiJ (male, 69 days) liver tissue; Mus musculus 129S1J (female, 72 days) heart tissue; ... and 126 more samples",
1280            "taxa": "Mus musculus",
1281            "treatments": []
1282        }
1283    ],
1284    "schema_version": "26",
1285    "sequencing_library_types": [
1286        "mRNA enriched"
1287    ],
1288    "status": "released",
1289    "strand_specificity": "5 prime to 3 prime",
1290    "submitted_by": {
1291        "@id": "/users/ebd1025b-e3ab-4e51-bfcd-1415f278281a/",
1292        "title": "Diane Trout"
1293    },
1294    "submitted_files_timestamp": "2023-10-06T03:40:46.186218+00:00",
1295    "summary": "Parse SPLiT-seq",
1296    "uuid": "b90a1709-514c-4c3c-bce5-69e37ccbdd9c"
1297}