substantia nigra — IGVFSM7602CRGV

1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM7602CRGV/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM7602CRGV",
11    "age": "76",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1833_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM7602CRGV](/tissues/IGVFSM7602CRGV/) 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/IGVFSM7602CRGV/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM7602CRGV](/tissues/IGVFSM7602CRGV/) 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/IGVFSM7602CRGV/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:15:21.795429+00:00",
44    "date_obtained": "2023-03-15",
45    "disease_terms": [
46        {
47            "@id": "/phenotype-terms/DOID_14330/",
48            "status": "in progress",
49            "term_name": "Parkinson's disease"
50        }
51    ],
52    "donors": [
53        {
54            "@id": "/human-donors/IGVFDO4812DEVH/",
55            "accession": "IGVFDO4812DEVH",
56            "ethnicities": [
57                "European"
58            ],
59            "status": "preview"
60        }
61    ],
62    "file_sets": [
63        {
64            "@id": "/measurement-sets/IGVFDS9165PGZO/",
65            "accession": "IGVFDS9165PGZO",
66            "aliases": [
67                "igvf:corces_measurementSet_X045_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/IGVFDS2373KVYV/",
79            "accession": "IGVFDS2373KVYV",
80            "aliases": [
81                "igvf:corces_measurementSet_X045_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/IGVFDS2994XKQR/",
93            "accession": "IGVFDS2994XKQR",
94            "aliases": [
95                "igvf:corces_measurementSet_X045_G6_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/IGVFDS8668VCFD/",
107            "accession": "IGVFDS8668VCFD",
108            "aliases": [
109                "igvf:corces_measurementSet_X045_G6_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/IGVFDS7412ZECB/",
121            "accession": "IGVFDS7412ZECB",
122            "aliases": [
123                "igvf:corces_measurementSet_X045_G5_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/IGVFDS9480SSTX/",
135            "accession": "IGVFDS9480SSTX",
136            "aliases": [
137                "igvf:corces_measurementSet_X045_G5_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/IGVFDS9847KZJV/",
149            "accession": "IGVFDS9847KZJV",
150            "aliases": [
151                "igvf:corces_measurementSet_X045_G7_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/IGVFDS0170SDNB/",
163            "accession": "IGVFDS0170SDNB",
164            "aliases": [
165                "igvf:corces_measurementSet_X045_G7_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/IGVFDS2244JUGR/",
177            "accession": "IGVFDS2244JUGR",
178            "aliases": [
179                "igvf:corces_measurementSet_X045_G1_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/IGVFDS3164XQLE/",
191            "accession": "IGVFDS3164XQLE",
192            "aliases": [
193                "igvf:corces_measurementSet_X045_G1_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/IGVFDS6181AGCI/",
205            "accession": "IGVFDS6181AGCI",
206            "aliases": [
207                "igvf:corces_measurementSet_X045_G3_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/IGVFDS3516DUWU/",
219            "accession": "IGVFDS3516DUWU",
220            "aliases": [
221                "igvf:corces_measurementSet_X045_G3_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/IGVFDS4033UDFN/",
233            "accession": "IGVFDS4033UDFN",
234            "aliases": [
235                "igvf:corces_measurementSet_X045_G8_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/IGVFDS2415CEXM/",
247            "accession": "IGVFDS2415CEXM",
248            "aliases": [
249                "igvf:corces_measurementSet_X045_G8_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/IGVFDS1106JKWP/",
261            "accession": "IGVFDS1106JKWP",
262            "aliases": [
263                "igvf:corces_measurementSet_X045_G4_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/IGVFDS7523ZOWN/",
275            "accession": "IGVFDS7523ZOWN",
276            "aliases": [
277                "igvf:corces_measurementSet_X045_G4_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/IGVFDS8528XJMX/",
289            "accession": "IGVFDS8528XJMX",
290            "aliases": [
291                "igvf:corces_measurementSet_RP018_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/IGVFDS8319TUBW/",
303            "accession": "IGVFDS8319TUBW",
304            "aliases": [
305                "igvf:corces_measurementSet_RP018_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/IGVFDS1869XCPD/",
317            "accession": "IGVFDS1869XCPD",
318            "aliases": [
319                "igvf:corces_measurementSet_RP018_G2_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/IGVFDS3371UYOY/",
331            "accession": "IGVFDS3371UYOY",
332            "aliases": [
333                "igvf:corces_measurementSet_RP018_G2_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/IGVFDS8112LERP/",
345            "accession": "IGVFDS8112LERP",
346            "aliases": [
347                "igvf:corces_measurementSet_RP018_G4_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/IGVFDS7572ZDYQ/",
359            "accession": "IGVFDS7572ZDYQ",
360            "aliases": [
361                "igvf:corces_measurementSet_RP018_G4_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/IGVFDS3423DTHY/",
373            "accession": "IGVFDS3423DTHY",
374            "aliases": [
375                "igvf:corces_measurementSet_RP018_G5_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/IGVFDS8678BJVO/",
387            "accession": "IGVFDS8678BJVO",
388            "aliases": [
389                "igvf:corces_measurementSet_RP018_G5_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            "@id": "/measurement-sets/IGVFDS4938ZDAY/",
401            "accession": "IGVFDS4938ZDAY",
402            "aliases": [
403                "igvf:corces_measurementSet_RP018_G6_ATAC"
404            ],
405            "file_set_type": "experimental data",
406            "lab": {
407                "title": "Ryan Corces, Gladstone Institute UCSF"
408            },
409            "preferred_assay_title": "10x multiome",
410            "status": "preview",
411            "summary": "single-nucleus ATAC-seq (10x multiome)"
412        },
413        {
414            "@id": "/measurement-sets/IGVFDS2371MSDM/",
415            "accession": "IGVFDS2371MSDM",
416            "aliases": [
417                "igvf:corces_measurementSet_RP018_G6_RNA"
418            ],
419            "file_set_type": "experimental data",
420            "lab": {
421                "title": "Ryan Corces, Gladstone Institute UCSF"
422            },
423            "preferred_assay_title": "10x multiome",
424            "status": "preview",
425            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
426        },
427        {
428            "@id": "/measurement-sets/IGVFDS2873YXDP/",
429            "accession": "IGVFDS2873YXDP",
430            "aliases": [
431                "igvf:corces_measurementSet_RP018_G3_ATAC"
432            ],
433            "file_set_type": "experimental data",
434            "lab": {
435                "title": "Ryan Corces, Gladstone Institute UCSF"
436            },
437            "preferred_assay_title": "10x multiome",
438            "status": "preview",
439            "summary": "single-nucleus ATAC-seq (10x multiome)"
440        },
441        {
442            "@id": "/measurement-sets/IGVFDS9355RKER/",
443            "accession": "IGVFDS9355RKER",
444            "aliases": [
445                "igvf:corces_measurementSet_RP018_G3_RNA"
446            ],
447            "file_set_type": "experimental data",
448            "lab": {
449                "title": "Ryan Corces, Gladstone Institute UCSF"
450            },
451            "preferred_assay_title": "10x multiome",
452            "status": "preview",
453            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
454        }
455    ],
456    "institutional_certificates": [
457        {
458            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
459            "certificate_identifier": "IP115-05",
460            "controlled_access": false,
461            "status": "in progress"
462        }
463    ],
464    "lab": {
465        "@id": "/labs/ryan-corces/",
466        "title": "Ryan Corces, Gladstone Institute UCSF"
467    },
468    "lower_bound_age": 76,
469    "lower_bound_age_in_hours": 665760,
470    "multiplexed_in": [
471        {
472            "@id": "/multiplexed-samples/IGVFSM4668ESUS/",
473            "accession": "IGVFSM4668ESUS",
474            "status": "preview"
475        },
476        {
477            "@id": "/multiplexed-samples/IGVFSM0962IVEP/",
478            "accession": "IGVFSM0962IVEP",
479            "status": "preview"
480        },
481        {
482            "@id": "/multiplexed-samples/IGVFSM5509EVZN/",
483            "accession": "IGVFSM5509EVZN",
484            "status": "preview"
485        },
486        {
487            "@id": "/multiplexed-samples/IGVFSM3071DTOY/",
488            "accession": "IGVFSM3071DTOY",
489            "status": "preview"
490        },
491        {
492            "@id": "/multiplexed-samples/IGVFSM2472IWEH/",
493            "accession": "IGVFSM2472IWEH",
494            "status": "preview"
495        },
496        {
497            "@id": "/multiplexed-samples/IGVFSM7137FCCD/",
498            "accession": "IGVFSM7137FCCD",
499            "status": "preview"
500        },
501        {
502            "@id": "/multiplexed-samples/IGVFSM3519VNVW/",
503            "accession": "IGVFSM3519VNVW",
504            "status": "preview"
505        },
506        {
507            "@id": "/multiplexed-samples/IGVFSM8872IRZA/",
508            "accession": "IGVFSM8872IRZA",
509            "status": "preview"
510        },
511        {
512            "@id": "/multiplexed-samples/IGVFSM3143GHVU/",
513            "accession": "IGVFSM3143GHVU",
514            "status": "preview"
515        },
516        {
517            "@id": "/multiplexed-samples/IGVFSM9675WPZF/",
518            "accession": "IGVFSM9675WPZF",
519            "status": "preview"
520        },
521        {
522            "@id": "/multiplexed-samples/IGVFSM1416OTQT/",
523            "accession": "IGVFSM1416OTQT",
524            "status": "preview"
525        },
526        {
527            "@id": "/multiplexed-samples/IGVFSM7137MKTX/",
528            "accession": "IGVFSM7137MKTX",
529            "status": "preview"
530        },
531        {
532            "@id": "/multiplexed-samples/IGVFSM4716JFLW/",
533            "accession": "IGVFSM4716JFLW",
534            "status": "preview"
535        },
536        {
537            "@id": "/multiplexed-samples/IGVFSM0275PBUR/",
538            "accession": "IGVFSM0275PBUR",
539            "status": "preview"
540        }
541    ],
542    "origin_of": [],
543    "parts": [],
544    "pmi": 198,
545    "pmi_units": "minute",
546    "pooled_in": [],
547    "preservation_method": "flash-freezing",
548    "protocols": [
549        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
550    ],
551    "sample_terms": [
552        {
553            "@id": "/sample-terms/UBERON_0002038/",
554            "status": "preview",
555            "term_name": "substantia nigra"
556        }
557    ],
558    "schema_version": "21",
559    "sex": "male",
560    "sorted_fractions": [],
561    "sources": [
562        {
563            "@id": "/sources/banner-health/",
564            "status": "released",
565            "title": "Banner Health"
566        }
567    ],
568    "status": "preview",
569    "submitted_by": {
570        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
571        "title": "Ryan Corces"
572    },
573    "summary": "Homo sapiens (male, 76 years) substantia nigra tissue associated with Parkinson's disease",
574    "taxa": "Homo sapiens",
575    "upper_bound_age": 76,
576    "upper_bound_age_in_hours": 665760,
577    "uuid": "6d3f5d03-af00-4b09-9830-31a01e6a46ea",
578    "virtual": false
579}