substantia nigra — IGVFSM8191RNGD

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM8191RNGD/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM8191RNGD",
11    "age": "84",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1973_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM8191RNGD](/tissues/IGVFSM8191RNGD/) 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/IGVFSM8191RNGD/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM8191RNGD](/tissues/IGVFSM8191RNGD/) 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/IGVFSM8191RNGD/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:11:17.822860+00:00",
44    "date_obtained": "2022-12-14",
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/IGVFDO0967LMSM/",
55            "accession": "IGVFDO0967LMSM",
56            "ethnicities": [
57                "European"
58            ],
59            "status": "preview"
60        }
61    ],
62    "file_sets": [
63        {
64            "@id": "/measurement-sets/IGVFDS3166POHS/",
65            "accession": "IGVFDS3166POHS",
66            "aliases": [
67                "igvf:corces_measurementSet_X025_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/IGVFDS8616NAOI/",
79            "accession": "IGVFDS8616NAOI",
80            "aliases": [
81                "igvf:corces_measurementSet_X025_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/IGVFDS0326OLER/",
93            "accession": "IGVFDS0326OLER",
94            "aliases": [
95                "igvf:corces_measurementSet_X025_G4_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/IGVFDS5286SAVD/",
107            "accession": "IGVFDS5286SAVD",
108            "aliases": [
109                "igvf:corces_measurementSet_X025_G4_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/IGVFDS0241TXPM/",
121            "accession": "IGVFDS0241TXPM",
122            "aliases": [
123                "igvf:corces_measurementSet_X025_G7_RNA"
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 RNA sequencing assay (10x multiome)"
132        },
133        {
134            "@id": "/measurement-sets/IGVFDS5478XCHL/",
135            "accession": "IGVFDS5478XCHL",
136            "aliases": [
137                "igvf:corces_measurementSet_X025_G7_ATAC"
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 ATAC-seq (10x multiome)"
146        },
147        {
148            "@id": "/measurement-sets/IGVFDS7226QHGC/",
149            "accession": "IGVFDS7226QHGC",
150            "aliases": [
151                "igvf:corces_measurementSet_X025_G6_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/IGVFDS9683XLIM/",
163            "accession": "IGVFDS9683XLIM",
164            "aliases": [
165                "igvf:corces_measurementSet_X025_G6_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/IGVFDS8438UHSY/",
177            "accession": "IGVFDS8438UHSY",
178            "aliases": [
179                "igvf:corces_measurementSet_X025_G3_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/IGVFDS3087IDPH/",
191            "accession": "IGVFDS3087IDPH",
192            "aliases": [
193                "igvf:corces_measurementSet_X025_G3_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/IGVFDS3593RLPT/",
205            "accession": "IGVFDS3593RLPT",
206            "aliases": [
207                "igvf:corces_measurementSet_X025_G1_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/IGVFDS2587POGO/",
219            "accession": "IGVFDS2587POGO",
220            "aliases": [
221                "igvf:corces_measurementSet_X025_G1_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/IGVFDS2414ATDI/",
233            "accession": "IGVFDS2414ATDI",
234            "aliases": [
235                "igvf:corces_measurementSet_X025_G5_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/IGVFDS7951HUGR/",
247            "accession": "IGVFDS7951HUGR",
248            "aliases": [
249                "igvf:corces_measurementSet_X025_G5_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/IGVFDS6783ZBOV/",
261            "accession": "IGVFDS6783ZBOV",
262            "aliases": [
263                "igvf:corces_measurementSet_RP009_G8_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/IGVFDS3214ILJT/",
275            "accession": "IGVFDS3214ILJT",
276            "aliases": [
277                "igvf:corces_measurementSet_RP009_G8_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/IGVFDS8552LVZZ/",
289            "accession": "IGVFDS8552LVZZ",
290            "aliases": [
291                "igvf:corces_measurementSet_RP009_G2_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/IGVFDS6296ORZC/",
303            "accession": "IGVFDS6296ORZC",
304            "aliases": [
305                "igvf:corces_measurementSet_RP009_G2_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/IGVFDS6561ZEIK/",
317            "accession": "IGVFDS6561ZEIK",
318            "aliases": [
319                "igvf:corces_measurementSet_RP009_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/IGVFDS8191ULWV/",
331            "accession": "IGVFDS8191ULWV",
332            "aliases": [
333                "igvf:corces_measurementSet_RP009_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/IGVFDS9247TMEL/",
345            "accession": "IGVFDS9247TMEL",
346            "aliases": [
347                "igvf:corces_measurementSet_RP009_G6_RNA"
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 RNA sequencing assay (10x multiome)"
356        },
357        {
358            "@id": "/measurement-sets/IGVFDS8957DHSL/",
359            "accession": "IGVFDS8957DHSL",
360            "aliases": [
361                "igvf:corces_measurementSet_RP009_G6_ATAC"
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 ATAC-seq (10x multiome)"
370        },
371        {
372            "@id": "/measurement-sets/IGVFDS9058STTC/",
373            "accession": "IGVFDS9058STTC",
374            "aliases": [
375                "igvf:corces_measurementSet_RP009_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/IGVFDS3397BHVF/",
387            "accession": "IGVFDS3397BHVF",
388            "aliases": [
389                "igvf:corces_measurementSet_RP009_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            "@id": "/measurement-sets/IGVFDS7477IHEZ/",
401            "accession": "IGVFDS7477IHEZ",
402            "aliases": [
403                "igvf:corces_measurementSet_RP009_G5_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/IGVFDS9755ETJZ/",
415            "accession": "IGVFDS9755ETJZ",
416            "aliases": [
417                "igvf:corces_measurementSet_RP009_G5_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/IGVFDS6455YIYD/",
429            "accession": "IGVFDS6455YIYD",
430            "aliases": [
431                "igvf:corces_measurementSet_RP009_G1_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/IGVFDS4675LCCM/",
443            "accession": "IGVFDS4675LCCM",
444            "aliases": [
445                "igvf:corces_measurementSet_RP009_G1_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            "@id": "/measurement-sets/IGVFDS5208BPDO/",
457            "accession": "IGVFDS5208BPDO",
458            "aliases": [
459                "igvf:corces_measurementSet_RP009_G7_ATAC"
460            ],
461            "file_set_type": "experimental data",
462            "lab": {
463                "title": "Ryan Corces, Gladstone Institute UCSF"
464            },
465            "preferred_assay_title": "10x multiome",
466            "status": "preview",
467            "summary": "single-nucleus ATAC-seq (10x multiome)"
468        },
469        {
470            "@id": "/measurement-sets/IGVFDS2993TBQL/",
471            "accession": "IGVFDS2993TBQL",
472            "aliases": [
473                "igvf:corces_measurementSet_RP009_G7_RNA"
474            ],
475            "file_set_type": "experimental data",
476            "lab": {
477                "title": "Ryan Corces, Gladstone Institute UCSF"
478            },
479            "preferred_assay_title": "10x multiome",
480            "status": "preview",
481            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
482        }
483    ],
484    "institutional_certificates": [
485        {
486            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
487            "certificate_identifier": "IP115-05",
488            "controlled_access": false,
489            "data_use_limitation_summary": "No limitations",
490            "status": "in progress"
491        }
492    ],
493    "lab": {
494        "@id": "/labs/ryan-corces/",
495        "title": "Ryan Corces, Gladstone Institute UCSF"
496    },
497    "lower_bound_age": 84,
498    "lower_bound_age_in_hours": 735840,
499    "multiplexed_in": [
500        {
501            "@id": "/multiplexed-samples/IGVFSM2452FKKK/",
502            "accession": "IGVFSM2452FKKK",
503            "status": "preview"
504        },
505        {
506            "@id": "/multiplexed-samples/IGVFSM5024AIVR/",
507            "accession": "IGVFSM5024AIVR",
508            "status": "preview"
509        },
510        {
511            "@id": "/multiplexed-samples/IGVFSM6749LEWH/",
512            "accession": "IGVFSM6749LEWH",
513            "status": "preview"
514        },
515        {
516            "@id": "/multiplexed-samples/IGVFSM6541UOZS/",
517            "accession": "IGVFSM6541UOZS",
518            "status": "preview"
519        },
520        {
521            "@id": "/multiplexed-samples/IGVFSM5411LEQJ/",
522            "accession": "IGVFSM5411LEQJ",
523            "status": "preview"
524        },
525        {
526            "@id": "/multiplexed-samples/IGVFSM7687WPSD/",
527            "accession": "IGVFSM7687WPSD",
528            "status": "in progress"
529        },
530        {
531            "@id": "/multiplexed-samples/IGVFSM6254TPHT/",
532            "accession": "IGVFSM6254TPHT",
533            "status": "preview"
534        },
535        {
536            "@id": "/multiplexed-samples/IGVFSM7611BPOR/",
537            "accession": "IGVFSM7611BPOR",
538            "status": "preview"
539        },
540        {
541            "@id": "/multiplexed-samples/IGVFSM9488DNCQ/",
542            "accession": "IGVFSM9488DNCQ",
543            "status": "preview"
544        },
545        {
546            "@id": "/multiplexed-samples/IGVFSM1206IWFU/",
547            "accession": "IGVFSM1206IWFU",
548            "status": "preview"
549        },
550        {
551            "@id": "/multiplexed-samples/IGVFSM6201VKVB/",
552            "accession": "IGVFSM6201VKVB",
553            "status": "preview"
554        },
555        {
556            "@id": "/multiplexed-samples/IGVFSM3263SQDP/",
557            "accession": "IGVFSM3263SQDP",
558            "status": "preview"
559        },
560        {
561            "@id": "/multiplexed-samples/IGVFSM9386ETNP/",
562            "accession": "IGVFSM9386ETNP",
563            "status": "preview"
564        },
565        {
566            "@id": "/multiplexed-samples/IGVFSM3999SNMB/",
567            "accession": "IGVFSM3999SNMB",
568            "status": "preview"
569        },
570        {
571            "@id": "/multiplexed-samples/IGVFSM3842WIDQ/",
572            "accession": "IGVFSM3842WIDQ",
573            "status": "preview"
574        },
575        {
576            "@id": "/multiplexed-samples/IGVFSM6972ZZKH/",
577            "accession": "IGVFSM6972ZZKH",
578            "status": "preview"
579        }
580    ],
581    "origin_of": [],
582    "parts": [],
583    "pmi": 223,
584    "pmi_units": "minute",
585    "pooled_in": [],
586    "preservation_method": "flash-freezing",
587    "protocols": [
588        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
589    ],
590    "sample_terms": [
591        {
592            "@id": "/sample-terms/UBERON_0002038/",
593            "status": "preview",
594            "term_name": "substantia nigra"
595        }
596    ],
597    "schema_version": "21",
598    "sex": "male",
599    "sorted_fractions": [],
600    "sources": [
601        {
602            "@id": "/sources/banner-health/",
603            "status": "released",
604            "title": "Banner Health"
605        }
606    ],
607    "status": "preview",
608    "submitted_by": {
609        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
610        "title": "Ryan Corces"
611    },
612    "summary": "Homo sapiens (male, 84 years) substantia nigra tissue associated with Parkinson's disease",
613    "taxa": "Homo sapiens",
614    "upper_bound_age": 84,
615    "upper_bound_age_in_hours": 735840,
616    "uuid": "67cb6fa7-097b-487d-bad4-d3552c0183cd",
617    "virtual": false
618}