IGVFDS2063ABVV

released
GRU
1{
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10    "aliases": [
11        "buenrostro-bernstein:scATAC Lib 549"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0002764/",
15        "assay_slims": [
16            "chromatin accessibility"
17        ],
18        "status": "released",
19        "term_name": "single-cell ATAC-seq"
20    },
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22        "INTERNAL_ACTION": [
23            {
24                "category": "missing publication",
25                "detail": "In vitro system [IGVFSM3378QHHI](/in-vitro-systems/IGVFSM3378QHHI/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
26                "level": 30,
27                "level_name": "INTERNAL_ACTION",
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29                "path": "/in-vitro-systems/IGVFSM3378QHHI/"
30            },
31            {
32                "category": "missing publication",
33                "detail": "Measurement set [IGVFDS2063ABVV](/measurement-sets/IGVFDS2063ABVV/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
34                "level": 30,
35                "level_name": "INTERNAL_ACTION",
36                "name": "audit_file_set_missing_publication",
37                "path": "/measurement-sets/IGVFDS2063ABVV/"
38            },
39            {
40                "category": "mismatched status",
41                "detail": "Released measurement set [IGVFDS2063ABVV](/measurement-sets/IGVFDS2063ABVV/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
42                "level": 30,
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44                "name": "audit_item_status",
45                "path": "/measurement-sets/IGVFDS2063ABVV/"
46            },
47            {
48                "category": "mismatched status",
49                "detail": "Released measurement set [IGVFDS2063ABVV](/measurement-sets/IGVFDS2063ABVV/) has in progress subobject tabular file [IGVFFI1312HTQX](/tabular-files/IGVFFI1312HTQX/).",
50                "level": 30,
51                "level_name": "INTERNAL_ACTION",
52                "name": "audit_item_status",
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54            }
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56    },
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59        "component": "mapping",
60        "contact_pi": {
61            "@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
62            "title": "Jason Buenrostro"
63        },
64        "title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
65    },
66    "control_for": [],
67    "controlled_access": true,
68    "creation_timestamp": "2024-08-20T15:00:52.751975+00:00",
69    "data_use_limitation_summaries": [
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88            ],
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92        },
93        {
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97                "buenrostro-bernstein:Donor 1787"
98            ],
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103        {
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105            "accession": "IGVFDO1255IJEH",
106            "aliases": [
107                "buenrostro-bernstein:Donor 1975"
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112        },
113        {
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115            "accession": "IGVFDO5046RYOV",
116            "aliases": [
117                "buenrostro-bernstein:Donor 1949"
118            ],
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121            "taxa": "Homo sapiens"
122        },
123        {
124            "@id": "/human-donors/IGVFDO8033HKMP/",
125            "accession": "IGVFDO8033HKMP",
126            "aliases": [
127                "buenrostro-bernstein:Donor 1947"
128            ],
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131            "taxa": "Homo sapiens"
132        },
133        {
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135            "accession": "IGVFDO4983SZXB",
136            "aliases": [
137                "buenrostro-bernstein:Donor 1988"
138            ],
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141            "taxa": "Homo sapiens"
142        },
143        {
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145            "accession": "IGVFDO2476MGFK",
146            "aliases": [
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148            ],
149            "sex": "unspecified",
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151            "taxa": "Homo sapiens"
152        },
153        {
154            "@id": "/human-donors/IGVFDO2540COFN/",
155            "accession": "IGVFDO2540COFN",
156            "aliases": [
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158            ],
159            "sex": "unspecified",
160            "status": "released",
161            "taxa": "Homo sapiens"
162        },
163        {
164            "@id": "/human-donors/IGVFDO0508COBR/",
165            "accession": "IGVFDO0508COBR",
166            "aliases": [
167                "buenrostro-bernstein:Donor 1963"
168            ],
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171            "taxa": "Homo sapiens"
172        },
173        {
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178            ],
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181            "taxa": "Homo sapiens"
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188            ],
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201            "taxa": "Homo sapiens"
202        },
203        {
204            "@id": "/human-donors/IGVFDO0279GJBF/",
205            "accession": "IGVFDO0279GJBF",
206            "aliases": [
207                "buenrostro-bernstein:Donor 1937"
208            ],
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211            "taxa": "Homo sapiens"
212        },
213        {
214            "@id": "/human-donors/IGVFDO8979DYIF/",
215            "accession": "IGVFDO8979DYIF",
216            "aliases": [
217                "buenrostro-bernstein:Donor 1743"
218            ],
219            "sex": "unspecified",
220            "status": "released",
221            "taxa": "Homo sapiens"
222        },
223        {
224            "@id": "/human-donors/IGVFDO0211CZWE/",
225            "accession": "IGVFDO0211CZWE",
226            "aliases": [
227                "buenrostro-bernstein:Donor 1909"
228            ],
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230            "status": "released",
231            "taxa": "Homo sapiens"
232        },
233        {
234            "@id": "/human-donors/IGVFDO3701XUXY/",
235            "accession": "IGVFDO3701XUXY",
236            "aliases": [
237                "buenrostro-bernstein:Donor 1959"
238            ],
239            "sex": "unspecified",
240            "status": "released",
241            "taxa": "Homo sapiens"
242        },
243        {
244            "@id": "/human-donors/IGVFDO9063CMXP/",
245            "accession": "IGVFDO9063CMXP",
246            "aliases": [
247                "buenrostro-bernstein:Donor 1979"
248            ],
249            "sex": "unspecified",
250            "status": "released",
251            "taxa": "Homo sapiens"
252        },
253        {
254            "@id": "/human-donors/IGVFDO4747GRSS/",
255            "accession": "IGVFDO4747GRSS",
256            "aliases": [
257                "buenrostro-bernstein:Donor 1910"
258            ],
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261            "taxa": "Homo sapiens"
262        },
263        {
264            "@id": "/human-donors/IGVFDO5934RGQS/",
265            "accession": "IGVFDO5934RGQS",
266            "aliases": [
267                "buenrostro-bernstein:Donor 1956"
268            ],
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275            "accession": "IGVFDO1512EGWF",
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288            ],
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291            "taxa": "Homo sapiens"
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298            ],
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303        {
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313        {
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315            "accession": "IGVFDO3385RWXZ",
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317                "buenrostro-bernstein:Donor 1780"
318            ],
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323        {
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325            "accession": "IGVFDO4283QEWA",
326            "aliases": [
327                "buenrostro-bernstein:Donor 1974"
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329            "sex": "unspecified",
330            "status": "released",
331            "taxa": "Homo sapiens"
332        },
333        {
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335            "accession": "IGVFDO6075RUJJ",
336            "aliases": [
337                "buenrostro-bernstein:Donor 1935"
338            ],
339            "sex": "unspecified",
340            "status": "released",
341            "taxa": "Homo sapiens"
342        },
343        {
344            "@id": "/human-donors/IGVFDO4092SMML/",
345            "accession": "IGVFDO4092SMML",
346            "aliases": [
347                "buenrostro-bernstein:Donor 1941"
348            ],
349            "sex": "unspecified",
350            "status": "released",
351            "taxa": "Homo sapiens"
352        },
353        {
354            "@id": "/human-donors/IGVFDO5249VKYA/",
355            "accession": "IGVFDO5249VKYA",
356            "aliases": [
357                "buenrostro-bernstein:Donor 1954"
358            ],
359            "sex": "unspecified",
360            "status": "released",
361            "taxa": "Homo sapiens"
362        },
363        {
364            "@id": "/human-donors/IGVFDO2967OWUY/",
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372        },
373        {
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381            "taxa": "Homo sapiens"
382        },
383        {
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390            "status": "released",
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392        },
393        {
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399            "sex": "unspecified",
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403        {
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426            "aliases": [
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429            "sex": "unspecified",
430            "status": "released",
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432        },
433        {
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442        },
443        {
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448            ],
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452        },
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466            "aliases": [
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468            ],
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478            ],
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481            "taxa": "Homo sapiens"
482        },
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485            "accession": "IGVFDO1467HGMO",
486            "aliases": [
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488            ],
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491            "taxa": "Homo sapiens"
492        },
493        {
494            "@id": "/human-donors/IGVFDO9835EEAJ/",
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498            ],
499            "sex": "unspecified",
500            "status": "released",
501            "taxa": "Homo sapiens"
502        },
503        {
504            "@id": "/human-donors/IGVFDO3006ZNMC/",
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506            "aliases": [
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508            ],
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510            "status": "released",
511            "taxa": "Homo sapiens"
512        },
513        {
514            "@id": "/human-donors/IGVFDO4207CTJX/",
515            "accession": "IGVFDO4207CTJX",
516            "aliases": [
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518            ],
519            "sex": "unspecified",
520            "status": "released",
521            "taxa": "Homo sapiens"
522        },
523        {
524            "@id": "/human-donors/IGVFDO8124AYVF/",
525            "accession": "IGVFDO8124AYVF",
526            "aliases": [
527                "buenrostro-bernstein:Donor 1740"
528            ],
529            "sex": "unspecified",
530            "status": "released",
531            "taxa": "Homo sapiens"
532        },
533        {
534            "@id": "/human-donors/IGVFDO9770WYQG/",
535            "accession": "IGVFDO9770WYQG",
536            "aliases": [
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538            ],
539            "sex": "unspecified",
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541            "taxa": "Homo sapiens"
542        },
543        {
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551            "taxa": "Homo sapiens"
552        },
553        {
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556            "aliases": [
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558            ],
559            "sex": "unspecified",
560            "status": "released",
561            "taxa": "Homo sapiens"
562        },
563        {
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568            ],
569            "sex": "unspecified",
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572        },
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582        },
583        {
584            "@id": "/human-donors/IGVFDO9956LYMG/",
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598            ],
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601            "taxa": "Homo sapiens"
602        },
603        {
604            "@id": "/human-donors/IGVFDO0417TJMX/",
605            "accession": "IGVFDO0417TJMX",
606            "aliases": [
607                "buenrostro-bernstein:Donor 1907"
608            ],
609            "sex": "unspecified",
610            "status": "released",
611            "taxa": "Homo sapiens"
612        },
613        {
614            "@id": "/human-donors/IGVFDO8004EZUP/",
615            "accession": "IGVFDO8004EZUP",
616            "aliases": [
617                "buenrostro-bernstein:Donor 1962"
618            ],
619            "sex": "unspecified",
620            "status": "released",
621            "taxa": "Homo sapiens"
622        },
623        {
624            "@id": "/human-donors/IGVFDO6183QMMP/",
625            "accession": "IGVFDO6183QMMP",
626            "aliases": [
627                "buenrostro-bernstein:Donor 1788"
628            ],
629            "sex": "unspecified",
630            "status": "released",
631            "taxa": "Homo sapiens"
632        },
633        {
634            "@id": "/human-donors/IGVFDO2583SIHN/",
635            "accession": "IGVFDO2583SIHN",
636            "aliases": [
637                "buenrostro-bernstein:Donor 1938"
638            ],
639            "sex": "unspecified",
640            "status": "released",
641            "taxa": "Homo sapiens"
642        },
643        {
644            "@id": "/human-donors/IGVFDO5566VPJU/",
645            "accession": "IGVFDO5566VPJU",
646            "aliases": [
647                "buenrostro-bernstein:Donor 1908"
648            ],
649            "sex": "unspecified",
650            "status": "released",
651            "taxa": "Homo sapiens"
652        },
653        {
654            "@id": "/human-donors/IGVFDO9815AMKV/",
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1888            "s3_uri": "s3://igvf-files/2025/03/28/83c8d7f5-081d-4a74-94e3-069f73e3f968/IGVFFI6962JJKN.yaml.gz",
1889            "status": "released",
1890            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/cirm/IGVFFI3192GSXC_seqspec.yaml.gz",
1891            "upload_status": "validated"
1892        },
1893        {
1894            "@id": "/configuration-files/IGVFFI9263EZON/",
1895            "accession": "IGVFFI9263EZON",
1896            "aliases": [
1897                "buenrostro-bernstein:SS-LS_8983_seqspec"
1898            ],
1899            "content_type": "seqspec",
1900            "creation_timestamp": "2025-03-28T19:40:26.740927+00:00",
1901            "file_format": "yaml",
1902            "file_size": 1331,
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1905            "s3_uri": "s3://igvf-files/2025/03/28/05ca53b0-15d8-4e56-ba6d-e46aed035193/IGVFFI9263EZON.yaml.gz",
1906            "status": "released",
1907            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/cirm/IGVFFI6199MOVC_seqspec.yaml.gz",
1908            "upload_status": "validated"
1909        },
1910        {
1911            "@id": "/configuration-files/IGVFFI0428NMOT/",
1912            "accession": "IGVFFI0428NMOT",
1913            "aliases": [
1914                "buenrostro-bernstein:SS-LS_8887_seqspec"
1915            ],
1916            "content_type": "seqspec",
1917            "creation_timestamp": "2025-03-28T19:25:35.699593+00:00",
1918            "file_format": "yaml",
1919            "file_size": 1332,
1920            "href": "/configuration-files/IGVFFI0428NMOT/@@download/IGVFFI0428NMOT.yaml.gz",
1921            "md5sum": "ab28f22f1b87a538562e134b84483a02",
1922            "s3_uri": "s3://igvf-files/2025/03/28/ea731208-e808-4a0b-9d5d-cebc36fb6e61/IGVFFI0428NMOT.yaml.gz",
1923            "status": "released",
1924            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/cirm/IGVFFI3026LIYK_seqspec.yaml.gz",
1925            "upload_status": "validated"
1926        }
1927    ],
1928    "input_for": [
1929        "/analysis-sets/IGVFDS5023OFYF/"
1930    ],
1931    "lab": {
1932        "@id": "/labs/jason-buenrostro/",
1933        "title": "Jason Buenrostro, Broad"
1934    },
1935    "multiome_size": 2,
1936    "onlist_files": [
1937        "/tabular-files/IGVFFI1312HTQX/",
1938        "/tabular-files/IGVFFI0400MBIM/"
1939    ],
1940    "onlist_method": "product",
1941    "preferred_assay_title": "SHARE-seq",
1942    "protocols": [
1943        "https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
1944    ],
1945    "related_multiome_datasets": [
1946        {
1947            "@id": "/measurement-sets/IGVFDS1473PTAO/",
1948            "accession": "IGVFDS1473PTAO",
1949            "status": "released"
1950        }
1951    ],
1952    "release_timestamp": "2025-04-22T04:09:28.103170+00:00",
1953    "samples": [
1954        {
1955            "@id": "/in-vitro-systems/IGVFSM3378QHHI/",
1956            "@type": [
1957                "InVitroSystem",
1958                "Biosample",
1959                "Sample",
1960                "Item"
1961            ],
1962            "accession": "IGVFSM3378QHHI",
1963            "aliases": [
1964                "buenrostro-bernstein:BioSam 4881_SS-PKR 199"
1965            ],
1966            "cellular_sub_pool": "SS-PKR 199",
1967            "classifications": [
1968                "pooled cell specimen",
1969                "differentiated cell specimen"
1970            ],
1971            "institutional_certificates": [
1972                {
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1974                    "certificate_identifier": "IP113-01",
1975                    "controlled_access": true,
1976                    "data_use_limitation": "GRU",
1977                    "status": "released"
1978                },
1979                {
1980                    "@id": "/institutional-certificates/31aa03ce-8ec8-409b-8a6c-c115297c10f4/",
1981                    "certificate_identifier": "IP113-02",
1982                    "controlled_access": true,
1983                    "data_use_limitation": "GRU",
1984                    "status": "released"
1985                },
1986                {
1987                    "@id": "/institutional-certificates/07b1e07f-a66a-4bd5-9c1a-a8632e734789/",
1988                    "certificate_identifier": "IP113-03",
1989                    "controlled_access": true,
1990                    "data_use_limitation": "GRU",
1991                    "status": "released"
1992                },
1993                {
1994                    "@id": "/institutional-certificates/3c3d7aa1-227e-43c8-8c68-2d3ad8e280b9/",
1995                    "certificate_identifier": "IP113-04",
1996                    "controlled_access": true,
1997                    "data_use_limitation": "GRU",
1998                    "status": "released"
1999                },
2000                {
2001                    "@id": "/institutional-certificates/dff99f30-9e29-4410-bdb4-eed4b70432cf/",
2002                    "certificate_identifier": "IP113-05",
2003                    "controlled_access": true,
2004                    "data_use_limitation": "GRU",
2005                    "status": "released"
2006                },
2007                {
2008                    "@id": "/institutional-certificates/10318039-d9e6-4dd0-8d92-4c551493b9fe/",
2009                    "certificate_identifier": "IP113-06",
2010                    "controlled_access": true,
2011                    "data_use_limitation": "GRU",
2012                    "status": "released"
2013                },
2014                {
2015                    "@id": "/institutional-certificates/32e245d0-ae4b-4334-b826-ed5bf00f111f/",
2016                    "certificate_identifier": "IP113-07",
2017                    "controlled_access": true,
2018                    "data_use_limitation": "GRU",
2019                    "status": "released"
2020                },
2021                {
2022                    "@id": "/institutional-certificates/35c8ed2e-cf1b-4cdd-a6ee-e766e7c3d954/",
2023                    "certificate_identifier": "IP113-08",
2024                    "controlled_access": true,
2025                    "data_use_limitation": "GRU",
2026                    "status": "released"
2027                },
2028                {
2029                    "@id": "/institutional-certificates/70134af2-c4fd-43b4-96a6-9133a119a715/",
2030                    "certificate_identifier": "IP113-09",
2031                    "controlled_access": true,
2032                    "data_use_limitation": "GRU",
2033                    "status": "released"
2034                },
2035                {
2036                    "@id": "/institutional-certificates/8a10acc0-7e24-4912-8833-10141ccf9b5f/",
2037                    "certificate_identifier": "IP113-10",
2038                    "controlled_access": true,
2039                    "data_use_limitation": "GRU",
2040                    "status": "released"
2041                },
2042                {
2043                    "@id": "/institutional-certificates/21c46421-0482-4d0d-ad82-99387fc6add6/",
2044                    "certificate_identifier": "IP113-11",
2045                    "controlled_access": true,
2046                    "data_use_limitation": "GRU",
2047                    "status": "released"
2048                },
2049                {
2050                    "@id": "/institutional-certificates/74917306-afc2-447b-88b2-a97e3e758518/",
2051                    "certificate_identifier": "IP113-15",
2052                    "controlled_access": true,
2053                    "data_use_limitation": "GRU",
2054                    "status": "released"
2055                },
2056                {
2057                    "@id": "/institutional-certificates/b117b3dd-25d9-4262-a262-630852050446/",
2058                    "certificate_identifier": "IP113-12",
2059                    "controlled_access": true,
2060                    "data_use_limitation": "GRU",
2061                    "status": "released"
2062                },
2063                {
2064                    "@id": "/institutional-certificates/ae438897-696e-4b7a-98a2-e72438a76b31/",
2065                    "certificate_identifier": "IP113-13",
2066                    "controlled_access": true,
2067                    "data_use_limitation": "GRU",
2068                    "status": "released"
2069                },
2070                {
2071                    "@id": "/institutional-certificates/4542d787-ea26-4176-b01c-5c45ca11b802/",
2072                    "certificate_identifier": "IP113-14",
2073                    "controlled_access": true,
2074                    "data_use_limitation": "GRU",
2075                    "status": "released"
2076                },
2077                {
2078                    "@id": "/institutional-certificates/fc5dc734-179b-45b8-bb32-e4f57a6bf59c/",
2079                    "certificate_identifier": "IP113-16",
2080                    "controlled_access": true,
2081                    "data_use_limitation": "GRU",
2082                    "status": "released"
2083                },
2084                {
2085                    "@id": "/institutional-certificates/ebddd6b0-c53f-4e05-a451-b5167df7cebd/",
2086                    "certificate_identifier": "IP113-18",
2087                    "controlled_access": true,
2088                    "data_use_limitation": "GRU",
2089                    "status": "released"
2090                },
2091                {
2092                    "@id": "/institutional-certificates/cf9e5e74-e4e6-40d4-bf04-c86fafe9d17e/",
2093                    "certificate_identifier": "IP113-17",
2094                    "controlled_access": true,
2095                    "data_use_limitation": "GRU",
2096                    "status": "released"
2097                },
2098                {
2099                    "@id": "/institutional-certificates/109b8309-9842-4caa-80f7-9f3d1be0c8c1/",
2100                    "certificate_identifier": "IP113-19",
2101                    "controlled_access": true,
2102                    "data_use_limitation": "GRU",
2103                    "status": "released"
2104                },
2105                {
2106                    "@id": "/institutional-certificates/d1431ff4-0095-49ba-a179-5fe34043afeb/",
2107                    "certificate_identifier": "IP113-20",
2108                    "controlled_access": true,
2109                    "data_use_limitation": "GRU",
2110                    "status": "released"
2111                }
2112            ],
2113            "sample_terms": [
2114                {
2115                    "@id": "/sample-terms/EFO_0004905/",
2116                    "@type": [
2117                        "SampleTerm",
2118                        "OntologyTerm",
2119                        "Item"
2120                    ],
2121                    "status": "released",
2122                    "summary": "induced pluripotent stem cell",
2123                    "term_name": "induced pluripotent stem cell"
2124                }
2125            ],
2126            "status": "released",
2127            "summary": "Homo sapiens induced pluripotent stem pooled differentiated cell specimen induced to neural progenitor cell for 5 days (cellular sub pool: SS-PKR 199)",
2128            "targeted_sample_term": {
2129                "@id": "/sample-terms/CL_0011020/",
2130                "status": "released",
2131                "term_name": "neural progenitor cell"
2132            },
2133            "taxa": "Homo sapiens"
2134        }
2135    ],
2136    "schema_version": "26",
2137    "status": "released",
2138    "submitted_by": {
2139        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
2140        "title": "Siddarth Wekhande"
2141    },
2142    "submitted_files_timestamp": "2024-08-20T15:25:15.230021+00:00",
2143    "summary": "single-cell ATAC-seq (SHARE-seq)",
2144    "uuid": "6f1ace04-9ac9-4edb-acdd-e295290a8460"
2145}