substantia nigra — IGVFSM0003OIAP

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM0003OIAP/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM0003OIAP",
11    "age": "82",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1546_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM0003OIAP](/tissues/IGVFSM0003OIAP/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_item_status",
24                "path": "/tissues/IGVFSM0003OIAP/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM0003OIAP](/tissues/IGVFSM0003OIAP/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_tissue_ccf_id",
32                "path": "/tissues/IGVFSM0003OIAP/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:14:01.106989+00:00",
44    "date_obtained": "2023-02-22",
45    "disease_terms": [
46        {
47            "@id": "/phenotype-terms/DOID_9246/",
48            "status": "in progress",
49            "term_name": "cerebral amyloid angiopathy"
50        }
51    ],
52    "donors": [
53        {
54            "@id": "/human-donors/IGVFDO8504RBEL/",
55            "accession": "IGVFDO8504RBEL",
56            "ethnicities": [
57                "European"
58            ],
59            "status": "preview"
60        }
61    ],
62    "file_sets": [
63        {
64            "@id": "/measurement-sets/IGVFDS9037WATJ/",
65            "accession": "IGVFDS9037WATJ",
66            "aliases": [
67                "igvf:corces_measurementSet_X039_G2_ATAC"
68            ],
69            "file_set_type": "experimental data",
70            "lab": {
71                "title": "Ryan Corces, Gladstone Institute UCSF"
72            },
73            "preferred_assay_title": "10x multiome",
74            "status": "preview",
75            "summary": "single-nucleus ATAC-seq (10x multiome)"
76        },
77        {
78            "@id": "/measurement-sets/IGVFDS2448KDEL/",
79            "accession": "IGVFDS2448KDEL",
80            "aliases": [
81                "igvf:corces_measurementSet_X039_G2_RNA"
82            ],
83            "file_set_type": "experimental data",
84            "lab": {
85                "title": "Ryan Corces, Gladstone Institute UCSF"
86            },
87            "preferred_assay_title": "10x multiome",
88            "status": "preview",
89            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
90        },
91        {
92            "@id": "/measurement-sets/IGVFDS3979YUTV/",
93            "accession": "IGVFDS3979YUTV",
94            "aliases": [
95                "igvf:corces_measurementSet_X039_G8_ATAC"
96            ],
97            "file_set_type": "experimental data",
98            "lab": {
99                "title": "Ryan Corces, Gladstone Institute UCSF"
100            },
101            "preferred_assay_title": "10x multiome",
102            "status": "preview",
103            "summary": "single-nucleus ATAC-seq (10x multiome)"
104        },
105        {
106            "@id": "/measurement-sets/IGVFDS3433MQHU/",
107            "accession": "IGVFDS3433MQHU",
108            "aliases": [
109                "igvf:corces_measurementSet_X039_G8_RNA"
110            ],
111            "file_set_type": "experimental data",
112            "lab": {
113                "title": "Ryan Corces, Gladstone Institute UCSF"
114            },
115            "preferred_assay_title": "10x multiome",
116            "status": "preview",
117            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
118        },
119        {
120            "@id": "/measurement-sets/IGVFDS3068NKFQ/",
121            "accession": "IGVFDS3068NKFQ",
122            "aliases": [
123                "igvf:corces_measurementSet_X039_G6_ATAC"
124            ],
125            "file_set_type": "experimental data",
126            "lab": {
127                "title": "Ryan Corces, Gladstone Institute UCSF"
128            },
129            "preferred_assay_title": "10x multiome",
130            "status": "preview",
131            "summary": "single-nucleus ATAC-seq (10x multiome)"
132        },
133        {
134            "@id": "/measurement-sets/IGVFDS9790ACKH/",
135            "accession": "IGVFDS9790ACKH",
136            "aliases": [
137                "igvf:corces_measurementSet_X039_G6_RNA"
138            ],
139            "file_set_type": "experimental data",
140            "lab": {
141                "title": "Ryan Corces, Gladstone Institute UCSF"
142            },
143            "preferred_assay_title": "10x multiome",
144            "status": "preview",
145            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
146        },
147        {
148            "@id": "/measurement-sets/IGVFDS0948OFTV/",
149            "accession": "IGVFDS0948OFTV",
150            "aliases": [
151                "igvf:corces_measurementSet_X039_G1_ATAC"
152            ],
153            "file_set_type": "experimental data",
154            "lab": {
155                "title": "Ryan Corces, Gladstone Institute UCSF"
156            },
157            "preferred_assay_title": "10x multiome",
158            "status": "preview",
159            "summary": "single-nucleus ATAC-seq (10x multiome)"
160        },
161        {
162            "@id": "/measurement-sets/IGVFDS3861RJLB/",
163            "accession": "IGVFDS3861RJLB",
164            "aliases": [
165                "igvf:corces_measurementSet_X039_G1_RNA"
166            ],
167            "file_set_type": "experimental data",
168            "lab": {
169                "title": "Ryan Corces, Gladstone Institute UCSF"
170            },
171            "preferred_assay_title": "10x multiome",
172            "status": "preview",
173            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
174        },
175        {
176            "@id": "/measurement-sets/IGVFDS4967SVTM/",
177            "accession": "IGVFDS4967SVTM",
178            "aliases": [
179                "igvf:corces_measurementSet_X039_G7_ATAC"
180            ],
181            "file_set_type": "experimental data",
182            "lab": {
183                "title": "Ryan Corces, Gladstone Institute UCSF"
184            },
185            "preferred_assay_title": "10x multiome",
186            "status": "preview",
187            "summary": "single-nucleus ATAC-seq (10x multiome)"
188        },
189        {
190            "@id": "/measurement-sets/IGVFDS6013DGAO/",
191            "accession": "IGVFDS6013DGAO",
192            "aliases": [
193                "igvf:corces_measurementSet_X039_G7_RNA"
194            ],
195            "file_set_type": "experimental data",
196            "lab": {
197                "title": "Ryan Corces, Gladstone Institute UCSF"
198            },
199            "preferred_assay_title": "10x multiome",
200            "status": "preview",
201            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
202        },
203        {
204            "@id": "/measurement-sets/IGVFDS2816YXCJ/",
205            "accession": "IGVFDS2816YXCJ",
206            "aliases": [
207                "igvf:corces_measurementSet_X039_G5_ATAC"
208            ],
209            "file_set_type": "experimental data",
210            "lab": {
211                "title": "Ryan Corces, Gladstone Institute UCSF"
212            },
213            "preferred_assay_title": "10x multiome",
214            "status": "preview",
215            "summary": "single-nucleus ATAC-seq (10x multiome)"
216        },
217        {
218            "@id": "/measurement-sets/IGVFDS8457JNIV/",
219            "accession": "IGVFDS8457JNIV",
220            "aliases": [
221                "igvf:corces_measurementSet_X039_G5_RNA"
222            ],
223            "file_set_type": "experimental data",
224            "lab": {
225                "title": "Ryan Corces, Gladstone Institute UCSF"
226            },
227            "preferred_assay_title": "10x multiome",
228            "status": "preview",
229            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
230        },
231        {
232            "@id": "/measurement-sets/IGVFDS6300CCBZ/",
233            "accession": "IGVFDS6300CCBZ",
234            "aliases": [
235                "igvf:corces_measurementSet_X039_G4_ATAC"
236            ],
237            "file_set_type": "experimental data",
238            "lab": {
239                "title": "Ryan Corces, Gladstone Institute UCSF"
240            },
241            "preferred_assay_title": "10x multiome",
242            "status": "preview",
243            "summary": "single-nucleus ATAC-seq (10x multiome)"
244        },
245        {
246            "@id": "/measurement-sets/IGVFDS8238EXJQ/",
247            "accession": "IGVFDS8238EXJQ",
248            "aliases": [
249                "igvf:corces_measurementSet_X039_G4_RNA"
250            ],
251            "file_set_type": "experimental data",
252            "lab": {
253                "title": "Ryan Corces, Gladstone Institute UCSF"
254            },
255            "preferred_assay_title": "10x multiome",
256            "status": "preview",
257            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
258        },
259        {
260            "@id": "/measurement-sets/IGVFDS7653EYZX/",
261            "accession": "IGVFDS7653EYZX",
262            "aliases": [
263                "igvf:corces_measurementSet_X039_G3_ATAC"
264            ],
265            "file_set_type": "experimental data",
266            "lab": {
267                "title": "Ryan Corces, Gladstone Institute UCSF"
268            },
269            "preferred_assay_title": "10x multiome",
270            "status": "preview",
271            "summary": "single-nucleus ATAC-seq (10x multiome)"
272        },
273        {
274            "@id": "/measurement-sets/IGVFDS8059TAGM/",
275            "accession": "IGVFDS8059TAGM",
276            "aliases": [
277                "igvf:corces_measurementSet_X039_G3_RNA"
278            ],
279            "file_set_type": "experimental data",
280            "lab": {
281                "title": "Ryan Corces, Gladstone Institute UCSF"
282            },
283            "preferred_assay_title": "10x multiome",
284            "status": "preview",
285            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
286        },
287        {
288            "@id": "/measurement-sets/IGVFDS5924IYTA/",
289            "accession": "IGVFDS5924IYTA",
290            "aliases": [
291                "igvf:corces_measurementSet_RP020_G1_ATAC"
292            ],
293            "file_set_type": "experimental data",
294            "lab": {
295                "title": "Ryan Corces, Gladstone Institute UCSF"
296            },
297            "preferred_assay_title": "10x multiome",
298            "status": "preview",
299            "summary": "single-nucleus ATAC-seq (10x multiome)"
300        },
301        {
302            "@id": "/measurement-sets/IGVFDS4772OGMJ/",
303            "accession": "IGVFDS4772OGMJ",
304            "aliases": [
305                "igvf:corces_measurementSet_RP020_G1_RNA"
306            ],
307            "file_set_type": "experimental data",
308            "lab": {
309                "title": "Ryan Corces, Gladstone Institute UCSF"
310            },
311            "preferred_assay_title": "10x multiome",
312            "status": "preview",
313            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
314        },
315        {
316            "@id": "/measurement-sets/IGVFDS9492OFMM/",
317            "accession": "IGVFDS9492OFMM",
318            "aliases": [
319                "igvf:corces_measurementSet_RP020_G3_ATAC"
320            ],
321            "file_set_type": "experimental data",
322            "lab": {
323                "title": "Ryan Corces, Gladstone Institute UCSF"
324            },
325            "preferred_assay_title": "10x multiome",
326            "status": "preview",
327            "summary": "single-nucleus ATAC-seq (10x multiome)"
328        },
329        {
330            "@id": "/measurement-sets/IGVFDS6715SKDT/",
331            "accession": "IGVFDS6715SKDT",
332            "aliases": [
333                "igvf:corces_measurementSet_RP020_G3_RNA"
334            ],
335            "file_set_type": "experimental data",
336            "lab": {
337                "title": "Ryan Corces, Gladstone Institute UCSF"
338            },
339            "preferred_assay_title": "10x multiome",
340            "status": "preview",
341            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
342        },
343        {
344            "@id": "/measurement-sets/IGVFDS0580MSQQ/",
345            "accession": "IGVFDS0580MSQQ",
346            "aliases": [
347                "igvf:corces_measurementSet_RP020_G2_ATAC"
348            ],
349            "file_set_type": "experimental data",
350            "lab": {
351                "title": "Ryan Corces, Gladstone Institute UCSF"
352            },
353            "preferred_assay_title": "10x multiome",
354            "status": "preview",
355            "summary": "single-nucleus ATAC-seq (10x multiome)"
356        },
357        {
358            "@id": "/measurement-sets/IGVFDS4662SOHV/",
359            "accession": "IGVFDS4662SOHV",
360            "aliases": [
361                "igvf:corces_measurementSet_RP020_G2_RNA"
362            ],
363            "file_set_type": "experimental data",
364            "lab": {
365                "title": "Ryan Corces, Gladstone Institute UCSF"
366            },
367            "preferred_assay_title": "10x multiome",
368            "status": "preview",
369            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
370        },
371        {
372            "@id": "/measurement-sets/IGVFDS4171ULFR/",
373            "accession": "IGVFDS4171ULFR",
374            "aliases": [
375                "igvf:corces_measurementSet_RP020_G4_ATAC"
376            ],
377            "file_set_type": "experimental data",
378            "lab": {
379                "title": "Ryan Corces, Gladstone Institute UCSF"
380            },
381            "preferred_assay_title": "10x multiome",
382            "status": "preview",
383            "summary": "single-nucleus ATAC-seq (10x multiome)"
384        },
385        {
386            "@id": "/measurement-sets/IGVFDS0646UHCO/",
387            "accession": "IGVFDS0646UHCO",
388            "aliases": [
389                "igvf:corces_measurementSet_RP020_G4_RNA"
390            ],
391            "file_set_type": "experimental data",
392            "lab": {
393                "title": "Ryan Corces, Gladstone Institute UCSF"
394            },
395            "preferred_assay_title": "10x multiome",
396            "status": "preview",
397            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
398        }
399    ],
400    "institutional_certificates": [
401        {
402            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
403            "certificate_identifier": "IP115-05",
404            "controlled_access": false,
405            "status": "in progress"
406        }
407    ],
408    "lab": {
409        "@id": "/labs/ryan-corces/",
410        "title": "Ryan Corces, Gladstone Institute UCSF"
411    },
412    "lower_bound_age": 82,
413    "lower_bound_age_in_hours": 718320,
414    "multiplexed_in": [
415        {
416            "@id": "/multiplexed-samples/IGVFSM9156NSGE/",
417            "accession": "IGVFSM9156NSGE",
418            "status": "preview"
419        },
420        {
421            "@id": "/multiplexed-samples/IGVFSM7812ERJN/",
422            "accession": "IGVFSM7812ERJN",
423            "status": "preview"
424        },
425        {
426            "@id": "/multiplexed-samples/IGVFSM4211DBUX/",
427            "accession": "IGVFSM4211DBUX",
428            "status": "preview"
429        },
430        {
431            "@id": "/multiplexed-samples/IGVFSM3629YHDD/",
432            "accession": "IGVFSM3629YHDD",
433            "status": "preview"
434        },
435        {
436            "@id": "/multiplexed-samples/IGVFSM7823HUBP/",
437            "accession": "IGVFSM7823HUBP",
438            "status": "preview"
439        },
440        {
441            "@id": "/multiplexed-samples/IGVFSM6375ILFJ/",
442            "accession": "IGVFSM6375ILFJ",
443            "status": "preview"
444        },
445        {
446            "@id": "/multiplexed-samples/IGVFSM2908VCJO/",
447            "accession": "IGVFSM2908VCJO",
448            "status": "preview"
449        },
450        {
451            "@id": "/multiplexed-samples/IGVFSM1761LAJP/",
452            "accession": "IGVFSM1761LAJP",
453            "status": "preview"
454        },
455        {
456            "@id": "/multiplexed-samples/IGVFSM7245NHUU/",
457            "accession": "IGVFSM7245NHUU",
458            "status": "preview"
459        },
460        {
461            "@id": "/multiplexed-samples/IGVFSM9011XOSL/",
462            "accession": "IGVFSM9011XOSL",
463            "status": "preview"
464        },
465        {
466            "@id": "/multiplexed-samples/IGVFSM9612VWVL/",
467            "accession": "IGVFSM9612VWVL",
468            "status": "preview"
469        },
470        {
471            "@id": "/multiplexed-samples/IGVFSM2478QXUD/",
472            "accession": "IGVFSM2478QXUD",
473            "status": "preview"
474        }
475    ],
476    "origin_of": [],
477    "parts": [],
478    "pmi": 124,
479    "pmi_units": "minute",
480    "pooled_in": [],
481    "preservation_method": "flash-freezing",
482    "protocols": [
483        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
484    ],
485    "sample_terms": [
486        {
487            "@id": "/sample-terms/UBERON_0002038/",
488            "status": "preview",
489            "term_name": "substantia nigra"
490        }
491    ],
492    "schema_version": "21",
493    "sex": "female",
494    "sorted_fractions": [],
495    "sources": [
496        {
497            "@id": "/sources/banner-health/",
498            "status": "released",
499            "title": "Banner Health"
500        }
501    ],
502    "status": "preview",
503    "submitted_by": {
504        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
505        "title": "Ryan Corces"
506    },
507    "summary": "Homo sapiens (female, 82 years) substantia nigra tissue associated with cerebral amyloid angiopathy",
508    "taxa": "Homo sapiens",
509    "upper_bound_age": 82,
510    "upper_bound_age_in_hours": 718320,
511    "uuid": "d71d2636-42af-4cb7-9d39-57c63589a0f9",
512    "virtual": false
513}