substantia nigra — IGVFSM9351KOFY

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM9351KOFY/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM9351KOFY",
11    "age": "90 or above",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN0348_SN_B2"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM9351KOFY](/tissues/IGVFSM9351KOFY/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_item_status",
24                "path": "/tissues/IGVFSM9351KOFY/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM9351KOFY](/tissues/IGVFSM9351KOFY/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_item_status",
32                "path": "/tissues/IGVFSM9351KOFY/"
33            },
34            {
35                "category": "missing CCF ID",
36                "detail": "Tissue [IGVFSM9351KOFY](/tissues/IGVFSM9351KOFY/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
37                "level": 30,
38                "level_name": "INTERNAL_ACTION",
39                "name": "audit_tissue_ccf_id",
40                "path": "/tissues/IGVFSM9351KOFY/"
41            }
42        ]
43    },
44    "award": {
45        "@id": "/awards/HG012076/",
46        "component": "mapping"
47    },
48    "classifications": [
49        "tissue"
50    ],
51    "creation_timestamp": "2025-03-19T12:58:40.332890+00:00",
52    "date_obtained": "2023-03-20",
53    "disease_terms": [
54        {
55            "@id": "/phenotype-terms/DOID_14330/",
56            "status": "in progress",
57            "term_name": "Parkinson's disease"
58        },
59        {
60            "@id": "/phenotype-terms/DOID_9246/",
61            "status": "in progress",
62            "term_name": "cerebral amyloid angiopathy"
63        }
64    ],
65    "donors": [
66        {
67            "@id": "/human-donors/IGVFDO3628ZBBZ/",
68            "accession": "IGVFDO3628ZBBZ",
69            "ethnicities": [
70                "European"
71            ],
72            "status": "preview"
73        }
74    ],
75    "file_sets": [
76        {
77            "@id": "/measurement-sets/IGVFDS2016YSTR/",
78            "accession": "IGVFDS2016YSTR",
79            "aliases": [
80                "igvf:corces_measurementSet_X048_G6_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/IGVFDS4005TPVC/",
92            "accession": "IGVFDS4005TPVC",
93            "aliases": [
94                "igvf:corces_measurementSet_X048_G6_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/IGVFDS0930ZDXI/",
106            "accession": "IGVFDS0930ZDXI",
107            "aliases": [
108                "igvf:corces_measurementSet_X048_G3_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/IGVFDS8384PDHI/",
120            "accession": "IGVFDS8384PDHI",
121            "aliases": [
122                "igvf:corces_measurementSet_X048_G3_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/IGVFDS3125EBYU/",
134            "accession": "IGVFDS3125EBYU",
135            "aliases": [
136                "igvf:corces_measurementSet_X048_G2_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/IGVFDS2892UJBV/",
148            "accession": "IGVFDS2892UJBV",
149            "aliases": [
150                "igvf:corces_measurementSet_X048_G2_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/IGVFDS4012MFKW/",
162            "accession": "IGVFDS4012MFKW",
163            "aliases": [
164                "igvf:corces_measurementSet_X048_G7_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/IGVFDS9367SSNX/",
176            "accession": "IGVFDS9367SSNX",
177            "aliases": [
178                "igvf:corces_measurementSet_X048_G7_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/IGVFDS0040WTQJ/",
190            "accession": "IGVFDS0040WTQJ",
191            "aliases": [
192                "igvf:corces_measurementSet_X048_G4_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/IGVFDS9500FZKX/",
204            "accession": "IGVFDS9500FZKX",
205            "aliases": [
206                "igvf:corces_measurementSet_X048_G4_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/IGVFDS1648GTHD/",
218            "accession": "IGVFDS1648GTHD",
219            "aliases": [
220                "igvf:corces_measurementSet_X048_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/IGVFDS5539DHYG/",
232            "accession": "IGVFDS5539DHYG",
233            "aliases": [
234                "igvf:corces_measurementSet_X048_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/IGVFDS4913NONJ/",
246            "accession": "IGVFDS4913NONJ",
247            "aliases": [
248                "igvf:corces_measurementSet_X048_G1_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/IGVFDS5068FHJE/",
260            "accession": "IGVFDS5068FHJE",
261            "aliases": [
262                "igvf:corces_measurementSet_X048_G1_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            "@id": "/measurement-sets/IGVFDS2613EUNR/",
274            "accession": "IGVFDS2613EUNR",
275            "aliases": [
276                "igvf:corces_measurementSet_X048_G5_ATAC"
277            ],
278            "file_set_type": "experimental data",
279            "lab": {
280                "title": "Ryan Corces, Gladstone Institute UCSF"
281            },
282            "preferred_assay_title": "10x multiome",
283            "status": "preview",
284            "summary": "single-nucleus ATAC-seq (10x multiome)"
285        },
286        {
287            "@id": "/measurement-sets/IGVFDS2614JDXX/",
288            "accession": "IGVFDS2614JDXX",
289            "aliases": [
290                "igvf:corces_measurementSet_X048_G5_RNA"
291            ],
292            "file_set_type": "experimental data",
293            "lab": {
294                "title": "Ryan Corces, Gladstone Institute UCSF"
295            },
296            "preferred_assay_title": "10x multiome",
297            "status": "preview",
298            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
299        }
300    ],
301    "institutional_certificates": [
302        {
303            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
304            "certificate_identifier": "IP115-05",
305            "controlled_access": false,
306            "status": "in progress"
307        }
308    ],
309    "lab": {
310        "@id": "/labs/ryan-corces/",
311        "title": "Ryan Corces, Gladstone Institute UCSF"
312    },
313    "lower_bound_age": 90,
314    "lower_bound_age_in_hours": 788400,
315    "multiplexed_in": [
316        {
317            "@id": "/multiplexed-samples/IGVFSM0720FCFJ/",
318            "accession": "IGVFSM0720FCFJ",
319            "status": "preview"
320        },
321        {
322            "@id": "/multiplexed-samples/IGVFSM0811HBAI/",
323            "accession": "IGVFSM0811HBAI",
324            "status": "preview"
325        },
326        {
327            "@id": "/multiplexed-samples/IGVFSM4666GHWA/",
328            "accession": "IGVFSM4666GHWA",
329            "status": "preview"
330        },
331        {
332            "@id": "/multiplexed-samples/IGVFSM2062JXFD/",
333            "accession": "IGVFSM2062JXFD",
334            "status": "preview"
335        },
336        {
337            "@id": "/multiplexed-samples/IGVFSM4516HJDD/",
338            "accession": "IGVFSM4516HJDD",
339            "status": "preview"
340        },
341        {
342            "@id": "/multiplexed-samples/IGVFSM6506JPYW/",
343            "accession": "IGVFSM6506JPYW",
344            "status": "preview"
345        },
346        {
347            "@id": "/multiplexed-samples/IGVFSM0003NWYI/",
348            "accession": "IGVFSM0003NWYI",
349            "status": "preview"
350        },
351        {
352            "@id": "/multiplexed-samples/IGVFSM6138EUGH/",
353            "accession": "IGVFSM6138EUGH",
354            "status": "preview"
355        }
356    ],
357    "origin_of": [],
358    "part_of": "/tissues/IGVFSM7961GIBP/",
359    "parts": [],
360    "pmi": 180,
361    "pmi_units": "minute",
362    "pooled_in": [],
363    "preservation_method": "flash-freezing",
364    "protocols": [
365        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
366    ],
367    "sample_terms": [
368        {
369            "@id": "/sample-terms/UBERON_0002038/",
370            "status": "preview",
371            "term_name": "substantia nigra"
372        }
373    ],
374    "schema_version": "21",
375    "sex": "male",
376    "sorted_fractions": [],
377    "sources": [
378        {
379            "@id": "/sources/banner-health/",
380            "status": "released",
381            "title": "Banner Health"
382        }
383    ],
384    "status": "preview",
385    "submitted_by": {
386        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
387        "title": "Ryan Corces"
388    },
389    "summary": "Homo sapiens (male, 90 or above years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy",
390    "taxa": "Homo sapiens",
391    "upper_bound_age": 90,
392    "upper_bound_age_in_hours": 788400,
393    "uuid": "261f9628-b381-4ca7-8a59-c88e61f2a373",
394    "virtual": false
395}