substantia nigra — IGVFSM3488YSTA

1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM3488YSTA/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM3488YSTA",
11    "age": "81",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN9702_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "missing CCF ID",
20                "detail": "Tissue [IGVFSM3488YSTA](/tissues/IGVFSM3488YSTA/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_tissue_ccf_id",
24                "path": "/tissues/IGVFSM3488YSTA/"
25            }
26        ]
27    },
28    "award": {
29        "@id": "/awards/HG012076/",
30        "component": "mapping"
31    },
32    "classifications": [
33        "tissue"
34    ],
35    "creation_timestamp": "2025-03-19T04:13:29.050406+00:00",
36    "date_obtained": "2023-02-13",
37    "donors": [
38        {
39            "@id": "/human-donors/IGVFDO4103FHPT/",
40            "accession": "IGVFDO4103FHPT",
41            "ethnicities": [
42                "European"
43            ],
44            "status": "preview"
45        }
46    ],
47    "file_sets": [
48        {
49            "@id": "/measurement-sets/IGVFDS4337OWGM/",
50            "accession": "IGVFDS4337OWGM",
51            "aliases": [
52                "igvf:corces_measurementSet_X036_G3_ATAC"
53            ],
54            "file_set_type": "experimental data",
55            "lab": {
56                "title": "Ryan Corces, Gladstone Institute UCSF"
57            },
58            "preferred_assay_title": "10x multiome",
59            "status": "preview",
60            "summary": "single-nucleus ATAC-seq (10x multiome)"
61        },
62        {
63            "@id": "/measurement-sets/IGVFDS8023VYVU/",
64            "accession": "IGVFDS8023VYVU",
65            "aliases": [
66                "igvf:corces_measurementSet_X036_G3_RNA"
67            ],
68            "file_set_type": "experimental data",
69            "lab": {
70                "title": "Ryan Corces, Gladstone Institute UCSF"
71            },
72            "preferred_assay_title": "10x multiome",
73            "status": "preview",
74            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
75        },
76        {
77            "@id": "/measurement-sets/IGVFDS8307GMHR/",
78            "accession": "IGVFDS8307GMHR",
79            "aliases": [
80                "igvf:corces_measurementSet_X036_G1_ATAC"
81            ],
82            "file_set_type": "experimental data",
83            "lab": {
84                "title": "Ryan Corces, Gladstone Institute UCSF"
85            },
86            "preferred_assay_title": "10x multiome",
87            "status": "preview",
88            "summary": "single-nucleus ATAC-seq (10x multiome)"
89        },
90        {
91            "@id": "/measurement-sets/IGVFDS4285RNMV/",
92            "accession": "IGVFDS4285RNMV",
93            "aliases": [
94                "igvf:corces_measurementSet_X036_G1_RNA"
95            ],
96            "file_set_type": "experimental data",
97            "lab": {
98                "title": "Ryan Corces, Gladstone Institute UCSF"
99            },
100            "preferred_assay_title": "10x multiome",
101            "status": "preview",
102            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
103        },
104        {
105            "@id": "/measurement-sets/IGVFDS1818PYSX/",
106            "accession": "IGVFDS1818PYSX",
107            "aliases": [
108                "igvf:corces_measurementSet_X036_G4_ATAC"
109            ],
110            "file_set_type": "experimental data",
111            "lab": {
112                "title": "Ryan Corces, Gladstone Institute UCSF"
113            },
114            "preferred_assay_title": "10x multiome",
115            "status": "preview",
116            "summary": "single-nucleus ATAC-seq (10x multiome)"
117        },
118        {
119            "@id": "/measurement-sets/IGVFDS8908JLLN/",
120            "accession": "IGVFDS8908JLLN",
121            "aliases": [
122                "igvf:corces_measurementSet_X036_G4_RNA"
123            ],
124            "file_set_type": "experimental data",
125            "lab": {
126                "title": "Ryan Corces, Gladstone Institute UCSF"
127            },
128            "preferred_assay_title": "10x multiome",
129            "status": "preview",
130            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
131        },
132        {
133            "@id": "/measurement-sets/IGVFDS0591ZXQW/",
134            "accession": "IGVFDS0591ZXQW",
135            "aliases": [
136                "igvf:corces_measurementSet_X036_G7_ATAC"
137            ],
138            "file_set_type": "experimental data",
139            "lab": {
140                "title": "Ryan Corces, Gladstone Institute UCSF"
141            },
142            "preferred_assay_title": "10x multiome",
143            "status": "preview",
144            "summary": "single-nucleus ATAC-seq (10x multiome)"
145        },
146        {
147            "@id": "/measurement-sets/IGVFDS9894BDTA/",
148            "accession": "IGVFDS9894BDTA",
149            "aliases": [
150                "igvf:corces_measurementSet_X036_G7_RNA"
151            ],
152            "file_set_type": "experimental data",
153            "lab": {
154                "title": "Ryan Corces, Gladstone Institute UCSF"
155            },
156            "preferred_assay_title": "10x multiome",
157            "status": "preview",
158            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
159        },
160        {
161            "@id": "/measurement-sets/IGVFDS2109BZLJ/",
162            "accession": "IGVFDS2109BZLJ",
163            "aliases": [
164                "igvf:corces_measurementSet_X036_G2_ATAC"
165            ],
166            "file_set_type": "experimental data",
167            "lab": {
168                "title": "Ryan Corces, Gladstone Institute UCSF"
169            },
170            "preferred_assay_title": "10x multiome",
171            "status": "preview",
172            "summary": "single-nucleus ATAC-seq (10x multiome)"
173        },
174        {
175            "@id": "/measurement-sets/IGVFDS9262YHXZ/",
176            "accession": "IGVFDS9262YHXZ",
177            "aliases": [
178                "igvf:corces_measurementSet_X036_G2_RNA"
179            ],
180            "file_set_type": "experimental data",
181            "lab": {
182                "title": "Ryan Corces, Gladstone Institute UCSF"
183            },
184            "preferred_assay_title": "10x multiome",
185            "status": "preview",
186            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
187        },
188        {
189            "@id": "/measurement-sets/IGVFDS3520MQEA/",
190            "accession": "IGVFDS3520MQEA",
191            "aliases": [
192                "igvf:corces_measurementSet_X036_G5_ATAC"
193            ],
194            "file_set_type": "experimental data",
195            "lab": {
196                "title": "Ryan Corces, Gladstone Institute UCSF"
197            },
198            "preferred_assay_title": "10x multiome",
199            "status": "preview",
200            "summary": "single-nucleus ATAC-seq (10x multiome)"
201        },
202        {
203            "@id": "/measurement-sets/IGVFDS1696QREL/",
204            "accession": "IGVFDS1696QREL",
205            "aliases": [
206                "igvf:corces_measurementSet_X036_G5_RNA"
207            ],
208            "file_set_type": "experimental data",
209            "lab": {
210                "title": "Ryan Corces, Gladstone Institute UCSF"
211            },
212            "preferred_assay_title": "10x multiome",
213            "status": "preview",
214            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
215        },
216        {
217            "@id": "/measurement-sets/IGVFDS1836FIIK/",
218            "accession": "IGVFDS1836FIIK",
219            "aliases": [
220                "igvf:corces_measurementSet_X036_G8_ATAC"
221            ],
222            "file_set_type": "experimental data",
223            "lab": {
224                "title": "Ryan Corces, Gladstone Institute UCSF"
225            },
226            "preferred_assay_title": "10x multiome",
227            "status": "preview",
228            "summary": "single-nucleus ATAC-seq (10x multiome)"
229        },
230        {
231            "@id": "/measurement-sets/IGVFDS7423GMVI/",
232            "accession": "IGVFDS7423GMVI",
233            "aliases": [
234                "igvf:corces_measurementSet_X036_G8_RNA"
235            ],
236            "file_set_type": "experimental data",
237            "lab": {
238                "title": "Ryan Corces, Gladstone Institute UCSF"
239            },
240            "preferred_assay_title": "10x multiome",
241            "status": "preview",
242            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
243        },
244        {
245            "@id": "/measurement-sets/IGVFDS0749RBHU/",
246            "accession": "IGVFDS0749RBHU",
247            "aliases": [
248                "igvf:corces_measurementSet_X036_G6_ATAC"
249            ],
250            "file_set_type": "experimental data",
251            "lab": {
252                "title": "Ryan Corces, Gladstone Institute UCSF"
253            },
254            "preferred_assay_title": "10x multiome",
255            "status": "preview",
256            "summary": "single-nucleus ATAC-seq (10x multiome)"
257        },
258        {
259            "@id": "/measurement-sets/IGVFDS6828EMUR/",
260            "accession": "IGVFDS6828EMUR",
261            "aliases": [
262                "igvf:corces_measurementSet_X036_G6_RNA"
263            ],
264            "file_set_type": "experimental data",
265            "lab": {
266                "title": "Ryan Corces, Gladstone Institute UCSF"
267            },
268            "preferred_assay_title": "10x multiome",
269            "status": "preview",
270            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
271        }
272    ],
273    "institutional_certificates": [
274        {
275            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
276            "certificate_identifier": "IP115-05",
277            "controlled_access": false,
278            "status": "in progress"
279        }
280    ],
281    "lab": {
282        "@id": "/labs/ryan-corces/",
283        "title": "Ryan Corces, Gladstone Institute UCSF"
284    },
285    "lower_bound_age": 81,
286    "lower_bound_age_in_hours": 709560,
287    "multiplexed_in": [
288        {
289            "@id": "/multiplexed-samples/IGVFSM8150RMYY/",
290            "accession": "IGVFSM8150RMYY",
291            "status": "preview"
292        },
293        {
294            "@id": "/multiplexed-samples/IGVFSM9323AIRS/",
295            "accession": "IGVFSM9323AIRS",
296            "status": "preview"
297        },
298        {
299            "@id": "/multiplexed-samples/IGVFSM8249LKNM/",
300            "accession": "IGVFSM8249LKNM",
301            "status": "preview"
302        },
303        {
304            "@id": "/multiplexed-samples/IGVFSM5231ZGKX/",
305            "accession": "IGVFSM5231ZGKX",
306            "status": "preview"
307        },
308        {
309            "@id": "/multiplexed-samples/IGVFSM2877SEAA/",
310            "accession": "IGVFSM2877SEAA",
311            "status": "preview"
312        },
313        {
314            "@id": "/multiplexed-samples/IGVFSM4264GFJZ/",
315            "accession": "IGVFSM4264GFJZ",
316            "status": "preview"
317        },
318        {
319            "@id": "/multiplexed-samples/IGVFSM5388VXZF/",
320            "accession": "IGVFSM5388VXZF",
321            "status": "preview"
322        },
323        {
324            "@id": "/multiplexed-samples/IGVFSM0887BJSQ/",
325            "accession": "IGVFSM0887BJSQ",
326            "status": "preview"
327        }
328    ],
329    "origin_of": [],
330    "parts": [],
331    "pmi": 165,
332    "pmi_units": "minute",
333    "pooled_in": [],
334    "preservation_method": "flash-freezing",
335    "protocols": [
336        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
337    ],
338    "sample_terms": [
339        {
340            "@id": "/sample-terms/UBERON_0002038/",
341            "status": "preview",
342            "term_name": "substantia nigra"
343        }
344    ],
345    "schema_version": "21",
346    "sex": "male",
347    "sorted_fractions": [],
348    "sources": [
349        {
350            "@id": "/sources/banner-health/",
351            "status": "released",
352            "title": "Banner Health"
353        }
354    ],
355    "status": "preview",
356    "submitted_by": {
357        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
358        "title": "Ryan Corces"
359    },
360    "summary": "Homo sapiens (male, 81 years) substantia nigra tissue",
361    "taxa": "Homo sapiens",
362    "upper_bound_age": 81,
363    "upper_bound_age_in_hours": 709560,
364    "uuid": "9c2dc153-9042-4142-94cf-e777d547b97a",
365    "virtual": false
366}