substantia nigra — IGVFSM2586GUMX

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM2586GUMX/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM2586GUMX",
11    "age": "85",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1083_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM2586GUMX](/tissues/IGVFSM2586GUMX/) 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/IGVFSM2586GUMX/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM2586GUMX](/tissues/IGVFSM2586GUMX/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_item_status",
32                "path": "/tissues/IGVFSM2586GUMX/"
33            },
34            {
35                "category": "missing CCF ID",
36                "detail": "Tissue [IGVFSM2586GUMX](/tissues/IGVFSM2586GUMX/) 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/IGVFSM2586GUMX/"
41            }
42        ]
43    },
44    "award": {
45        "@id": "/awards/HG012076/",
46        "component": "mapping"
47    },
48    "classifications": [
49        "tissue"
50    ],
51    "creation_timestamp": "2025-03-19T04:10:09.349989+00:00",
52    "date_obtained": "2022-11-22",
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_0080832/",
61            "status": "in progress",
62            "term_name": "mild cognitive impairment"
63        }
64    ],
65    "donors": [
66        {
67            "@id": "/human-donors/IGVFDO3500WGWY/",
68            "accession": "IGVFDO3500WGWY",
69            "ethnicities": [
70                "European"
71            ],
72            "status": "preview"
73        }
74    ],
75    "file_sets": [
76        {
77            "@id": "/measurement-sets/IGVFDS4661FUFW/",
78            "accession": "IGVFDS4661FUFW",
79            "aliases": [
80                "igvf:corces_measurementSet_X018_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/IGVFDS8385AJOG/",
92            "accession": "IGVFDS8385AJOG",
93            "aliases": [
94                "igvf:corces_measurementSet_X018_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/IGVFDS5398QLMU/",
106            "accession": "IGVFDS5398QLMU",
107            "aliases": [
108                "igvf:corces_measurementSet_X018_G2_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/IGVFDS3606KJNK/",
120            "accession": "IGVFDS3606KJNK",
121            "aliases": [
122                "igvf:corces_measurementSet_X018_G2_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/IGVFDS6716ODJI/",
134            "accession": "IGVFDS6716ODJI",
135            "aliases": [
136                "igvf:corces_measurementSet_X018_G5_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/IGVFDS6107ITVM/",
148            "accession": "IGVFDS6107ITVM",
149            "aliases": [
150                "igvf:corces_measurementSet_X018_G5_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/IGVFDS7460ZJLL/",
162            "accession": "IGVFDS7460ZJLL",
163            "aliases": [
164                "igvf:corces_measurementSet_X018_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/IGVFDS4267COKK/",
176            "accession": "IGVFDS4267COKK",
177            "aliases": [
178                "igvf:corces_measurementSet_X018_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/IGVFDS8509DVUL/",
190            "accession": "IGVFDS8509DVUL",
191            "aliases": [
192                "igvf:corces_measurementSet_X018_G8_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/IGVFDS5209HPZQ/",
204            "accession": "IGVFDS5209HPZQ",
205            "aliases": [
206                "igvf:corces_measurementSet_X018_G8_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/IGVFDS8282BSIR/",
218            "accession": "IGVFDS8282BSIR",
219            "aliases": [
220                "igvf:corces_measurementSet_X018_G3_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/IGVFDS6864WUVY/",
232            "accession": "IGVFDS6864WUVY",
233            "aliases": [
234                "igvf:corces_measurementSet_X018_G3_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/IGVFDS3229AGXN/",
246            "accession": "IGVFDS3229AGXN",
247            "aliases": [
248                "igvf:corces_measurementSet_X018_G4_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/IGVFDS3746KFOG/",
260            "accession": "IGVFDS3746KFOG",
261            "aliases": [
262                "igvf:corces_measurementSet_X018_G4_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/IGVFDS8237XHKO/",
274            "accession": "IGVFDS8237XHKO",
275            "aliases": [
276                "igvf:corces_measurementSet_X018_G6_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/IGVFDS3609ZOOP/",
288            "accession": "IGVFDS3609ZOOP",
289            "aliases": [
290                "igvf:corces_measurementSet_X018_G6_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            "@id": "/measurement-sets/IGVFDS8859FDEI/",
302            "accession": "IGVFDS8859FDEI",
303            "aliases": [
304                "igvf:corces_measurementSet_RP015_G2_ATAC"
305            ],
306            "file_set_type": "experimental data",
307            "lab": {
308                "title": "Ryan Corces, Gladstone Institute UCSF"
309            },
310            "preferred_assay_title": "10x multiome",
311            "status": "preview",
312            "summary": "single-nucleus ATAC-seq (10x multiome)"
313        },
314        {
315            "@id": "/measurement-sets/IGVFDS9670KNNR/",
316            "accession": "IGVFDS9670KNNR",
317            "aliases": [
318                "igvf:corces_measurementSet_RP015_G2_RNA"
319            ],
320            "file_set_type": "experimental data",
321            "lab": {
322                "title": "Ryan Corces, Gladstone Institute UCSF"
323            },
324            "preferred_assay_title": "10x multiome",
325            "status": "preview",
326            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
327        },
328        {
329            "@id": "/measurement-sets/IGVFDS1451RVGA/",
330            "accession": "IGVFDS1451RVGA",
331            "aliases": [
332                "igvf:corces_measurementSet_RP015_G3_ATAC"
333            ],
334            "file_set_type": "experimental data",
335            "lab": {
336                "title": "Ryan Corces, Gladstone Institute UCSF"
337            },
338            "preferred_assay_title": "10x multiome",
339            "status": "preview",
340            "summary": "single-nucleus ATAC-seq (10x multiome)"
341        },
342        {
343            "@id": "/measurement-sets/IGVFDS0488NVQB/",
344            "accession": "IGVFDS0488NVQB",
345            "aliases": [
346                "igvf:corces_measurementSet_RP015_G3_RNA"
347            ],
348            "file_set_type": "experimental data",
349            "lab": {
350                "title": "Ryan Corces, Gladstone Institute UCSF"
351            },
352            "preferred_assay_title": "10x multiome",
353            "status": "preview",
354            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
355        },
356        {
357            "@id": "/measurement-sets/IGVFDS0737RQRG/",
358            "accession": "IGVFDS0737RQRG",
359            "aliases": [
360                "igvf:corces_measurementSet_RP015_G4_ATAC"
361            ],
362            "file_set_type": "experimental data",
363            "lab": {
364                "title": "Ryan Corces, Gladstone Institute UCSF"
365            },
366            "preferred_assay_title": "10x multiome",
367            "status": "preview",
368            "summary": "single-nucleus ATAC-seq (10x multiome)"
369        },
370        {
371            "@id": "/measurement-sets/IGVFDS7340HYVJ/",
372            "accession": "IGVFDS7340HYVJ",
373            "aliases": [
374                "igvf:corces_measurementSet_RP015_G4_RNA"
375            ],
376            "file_set_type": "experimental data",
377            "lab": {
378                "title": "Ryan Corces, Gladstone Institute UCSF"
379            },
380            "preferred_assay_title": "10x multiome",
381            "status": "preview",
382            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
383        },
384        {
385            "@id": "/measurement-sets/IGVFDS9379ZJGH/",
386            "accession": "IGVFDS9379ZJGH",
387            "aliases": [
388                "igvf:corces_measurementSet_RP015_G1_ATAC"
389            ],
390            "file_set_type": "experimental data",
391            "lab": {
392                "title": "Ryan Corces, Gladstone Institute UCSF"
393            },
394            "preferred_assay_title": "10x multiome",
395            "status": "preview",
396            "summary": "single-nucleus ATAC-seq (10x multiome)"
397        },
398        {
399            "@id": "/measurement-sets/IGVFDS2939KDMY/",
400            "accession": "IGVFDS2939KDMY",
401            "aliases": [
402                "igvf:corces_measurementSet_RP015_G1_RNA"
403            ],
404            "file_set_type": "experimental data",
405            "lab": {
406                "title": "Ryan Corces, Gladstone Institute UCSF"
407            },
408            "preferred_assay_title": "10x multiome",
409            "status": "preview",
410            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
411        }
412    ],
413    "institutional_certificates": [
414        {
415            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
416            "certificate_identifier": "IP115-05",
417            "controlled_access": false,
418            "status": "in progress"
419        }
420    ],
421    "lab": {
422        "@id": "/labs/ryan-corces/",
423        "title": "Ryan Corces, Gladstone Institute UCSF"
424    },
425    "lower_bound_age": 85,
426    "lower_bound_age_in_hours": 744600,
427    "multiplexed_in": [
428        {
429            "@id": "/multiplexed-samples/IGVFSM3747OUVO/",
430            "accession": "IGVFSM3747OUVO",
431            "status": "preview"
432        },
433        {
434            "@id": "/multiplexed-samples/IGVFSM9798GLTM/",
435            "accession": "IGVFSM9798GLTM",
436            "status": "preview"
437        },
438        {
439            "@id": "/multiplexed-samples/IGVFSM7341PDKY/",
440            "accession": "IGVFSM7341PDKY",
441            "status": "preview"
442        },
443        {
444            "@id": "/multiplexed-samples/IGVFSM6380FYLN/",
445            "accession": "IGVFSM6380FYLN",
446            "status": "preview"
447        },
448        {
449            "@id": "/multiplexed-samples/IGVFSM5218YFIX/",
450            "accession": "IGVFSM5218YFIX",
451            "status": "preview"
452        },
453        {
454            "@id": "/multiplexed-samples/IGVFSM3692IOZZ/",
455            "accession": "IGVFSM3692IOZZ",
456            "status": "preview"
457        },
458        {
459            "@id": "/multiplexed-samples/IGVFSM7256WFWF/",
460            "accession": "IGVFSM7256WFWF",
461            "status": "preview"
462        },
463        {
464            "@id": "/multiplexed-samples/IGVFSM8022FKWE/",
465            "accession": "IGVFSM8022FKWE",
466            "status": "preview"
467        },
468        {
469            "@id": "/multiplexed-samples/IGVFSM3324TBYQ/",
470            "accession": "IGVFSM3324TBYQ",
471            "status": "preview"
472        },
473        {
474            "@id": "/multiplexed-samples/IGVFSM0903NROD/",
475            "accession": "IGVFSM0903NROD",
476            "status": "preview"
477        },
478        {
479            "@id": "/multiplexed-samples/IGVFSM0218TRNG/",
480            "accession": "IGVFSM0218TRNG",
481            "status": "preview"
482        },
483        {
484            "@id": "/multiplexed-samples/IGVFSM1969WJDB/",
485            "accession": "IGVFSM1969WJDB",
486            "status": "preview"
487        }
488    ],
489    "origin_of": [],
490    "parts": [],
491    "pmi": 165,
492    "pmi_units": "minute",
493    "pooled_in": [],
494    "preservation_method": "flash-freezing",
495    "protocols": [
496        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
497    ],
498    "sample_terms": [
499        {
500            "@id": "/sample-terms/UBERON_0002038/",
501            "status": "preview",
502            "term_name": "substantia nigra"
503        }
504    ],
505    "schema_version": "21",
506    "sex": "male",
507    "sorted_fractions": [],
508    "sources": [
509        {
510            "@id": "/sources/banner-health/",
511            "status": "released",
512            "title": "Banner Health"
513        }
514    ],
515    "status": "preview",
516    "submitted_by": {
517        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
518        "title": "Ryan Corces"
519    },
520    "summary": "Homo sapiens (male, 85 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment",
521    "taxa": "Homo sapiens",
522    "upper_bound_age": 85,
523    "upper_bound_age_in_hours": 744600,
524    "uuid": "00b2f920-ef37-416b-bf81-3aa876f40f34",
525    "virtual": false
526}