substantia nigra — IGVFSM4726MNFB

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM4726MNFB/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM4726MNFB",
11    "age": "72",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1864_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM4726MNFB](/tissues/IGVFSM4726MNFB/) 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/IGVFSM4726MNFB/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM4726MNFB](/tissues/IGVFSM4726MNFB/) 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/IGVFSM4726MNFB/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:14:44.146683+00:00",
44    "date_obtained": "2023-03-09",
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/IGVFDO4170HAEN/",
55            "accession": "IGVFDO4170HAEN",
56            "status": "preview"
57        }
58    ],
59    "file_sets": [
60        {
61            "@id": "/measurement-sets/IGVFDS3148PUJM/",
62            "accession": "IGVFDS3148PUJM",
63            "aliases": [
64                "igvf:corces_measurementSet_X042_G7_ATAC"
65            ],
66            "file_set_type": "experimental data",
67            "lab": {
68                "title": "Ryan Corces, Gladstone Institute UCSF"
69            },
70            "preferred_assay_title": "10x multiome",
71            "status": "preview",
72            "summary": "single-nucleus ATAC-seq (10x multiome)"
73        },
74        {
75            "@id": "/measurement-sets/IGVFDS0551JWHB/",
76            "accession": "IGVFDS0551JWHB",
77            "aliases": [
78                "igvf:corces_measurementSet_X042_G7_RNA"
79            ],
80            "file_set_type": "experimental data",
81            "lab": {
82                "title": "Ryan Corces, Gladstone Institute UCSF"
83            },
84            "preferred_assay_title": "10x multiome",
85            "status": "preview",
86            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
87        },
88        {
89            "@id": "/measurement-sets/IGVFDS6059WKSH/",
90            "accession": "IGVFDS6059WKSH",
91            "aliases": [
92                "igvf:corces_measurementSet_X042_G5_ATAC"
93            ],
94            "file_set_type": "experimental data",
95            "lab": {
96                "title": "Ryan Corces, Gladstone Institute UCSF"
97            },
98            "preferred_assay_title": "10x multiome",
99            "status": "preview",
100            "summary": "single-nucleus ATAC-seq (10x multiome)"
101        },
102        {
103            "@id": "/measurement-sets/IGVFDS5672IBLK/",
104            "accession": "IGVFDS5672IBLK",
105            "aliases": [
106                "igvf:corces_measurementSet_X042_G5_RNA"
107            ],
108            "file_set_type": "experimental data",
109            "lab": {
110                "title": "Ryan Corces, Gladstone Institute UCSF"
111            },
112            "preferred_assay_title": "10x multiome",
113            "status": "preview",
114            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
115        },
116        {
117            "@id": "/measurement-sets/IGVFDS5571QAYO/",
118            "accession": "IGVFDS5571QAYO",
119            "aliases": [
120                "igvf:corces_measurementSet_X042_G3_ATAC"
121            ],
122            "file_set_type": "experimental data",
123            "lab": {
124                "title": "Ryan Corces, Gladstone Institute UCSF"
125            },
126            "preferred_assay_title": "10x multiome",
127            "status": "preview",
128            "summary": "single-nucleus ATAC-seq (10x multiome)"
129        },
130        {
131            "@id": "/measurement-sets/IGVFDS8148USUN/",
132            "accession": "IGVFDS8148USUN",
133            "aliases": [
134                "igvf:corces_measurementSet_X042_G3_RNA"
135            ],
136            "file_set_type": "experimental data",
137            "lab": {
138                "title": "Ryan Corces, Gladstone Institute UCSF"
139            },
140            "preferred_assay_title": "10x multiome",
141            "status": "preview",
142            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
143        },
144        {
145            "@id": "/measurement-sets/IGVFDS3141FRLK/",
146            "accession": "IGVFDS3141FRLK",
147            "aliases": [
148                "igvf:corces_measurementSet_X042_G4_ATAC"
149            ],
150            "file_set_type": "experimental data",
151            "lab": {
152                "title": "Ryan Corces, Gladstone Institute UCSF"
153            },
154            "preferred_assay_title": "10x multiome",
155            "status": "preview",
156            "summary": "single-nucleus ATAC-seq (10x multiome)"
157        },
158        {
159            "@id": "/measurement-sets/IGVFDS6532IRJT/",
160            "accession": "IGVFDS6532IRJT",
161            "aliases": [
162                "igvf:corces_measurementSet_X042_G4_RNA"
163            ],
164            "file_set_type": "experimental data",
165            "lab": {
166                "title": "Ryan Corces, Gladstone Institute UCSF"
167            },
168            "preferred_assay_title": "10x multiome",
169            "status": "preview",
170            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
171        },
172        {
173            "@id": "/measurement-sets/IGVFDS6932ECNS/",
174            "accession": "IGVFDS6932ECNS",
175            "aliases": [
176                "igvf:corces_measurementSet_X042_G6_ATAC"
177            ],
178            "file_set_type": "experimental data",
179            "lab": {
180                "title": "Ryan Corces, Gladstone Institute UCSF"
181            },
182            "preferred_assay_title": "10x multiome",
183            "status": "preview",
184            "summary": "single-nucleus ATAC-seq (10x multiome)"
185        },
186        {
187            "@id": "/measurement-sets/IGVFDS8894MIXR/",
188            "accession": "IGVFDS8894MIXR",
189            "aliases": [
190                "igvf:corces_measurementSet_X042_G6_RNA"
191            ],
192            "file_set_type": "experimental data",
193            "lab": {
194                "title": "Ryan Corces, Gladstone Institute UCSF"
195            },
196            "preferred_assay_title": "10x multiome",
197            "status": "preview",
198            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
199        },
200        {
201            "@id": "/measurement-sets/IGVFDS0978UQYD/",
202            "accession": "IGVFDS0978UQYD",
203            "aliases": [
204                "igvf:corces_measurementSet_X042_G8_ATAC"
205            ],
206            "file_set_type": "experimental data",
207            "lab": {
208                "title": "Ryan Corces, Gladstone Institute UCSF"
209            },
210            "preferred_assay_title": "10x multiome",
211            "status": "preview",
212            "summary": "single-nucleus ATAC-seq (10x multiome)"
213        },
214        {
215            "@id": "/measurement-sets/IGVFDS2377SEOL/",
216            "accession": "IGVFDS2377SEOL",
217            "aliases": [
218                "igvf:corces_measurementSet_X042_G8_RNA"
219            ],
220            "file_set_type": "experimental data",
221            "lab": {
222                "title": "Ryan Corces, Gladstone Institute UCSF"
223            },
224            "preferred_assay_title": "10x multiome",
225            "status": "preview",
226            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
227        },
228        {
229            "@id": "/measurement-sets/IGVFDS3959TIPT/",
230            "accession": "IGVFDS3959TIPT",
231            "aliases": [
232                "igvf:corces_measurementSet_X042_G1_ATAC"
233            ],
234            "file_set_type": "experimental data",
235            "lab": {
236                "title": "Ryan Corces, Gladstone Institute UCSF"
237            },
238            "preferred_assay_title": "10x multiome",
239            "status": "preview",
240            "summary": "single-nucleus ATAC-seq (10x multiome)"
241        },
242        {
243            "@id": "/measurement-sets/IGVFDS8659VRHH/",
244            "accession": "IGVFDS8659VRHH",
245            "aliases": [
246                "igvf:corces_measurementSet_X042_G1_RNA"
247            ],
248            "file_set_type": "experimental data",
249            "lab": {
250                "title": "Ryan Corces, Gladstone Institute UCSF"
251            },
252            "preferred_assay_title": "10x multiome",
253            "status": "preview",
254            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
255        },
256        {
257            "@id": "/measurement-sets/IGVFDS1395GBFX/",
258            "accession": "IGVFDS1395GBFX",
259            "aliases": [
260                "igvf:corces_measurementSet_X042_G2_ATAC"
261            ],
262            "file_set_type": "experimental data",
263            "lab": {
264                "title": "Ryan Corces, Gladstone Institute UCSF"
265            },
266            "preferred_assay_title": "10x multiome",
267            "status": "preview",
268            "summary": "single-nucleus ATAC-seq (10x multiome)"
269        },
270        {
271            "@id": "/measurement-sets/IGVFDS8219ZWGY/",
272            "accession": "IGVFDS8219ZWGY",
273            "aliases": [
274                "igvf:corces_measurementSet_X042_G2_RNA"
275            ],
276            "file_set_type": "experimental data",
277            "lab": {
278                "title": "Ryan Corces, Gladstone Institute UCSF"
279            },
280            "preferred_assay_title": "10x multiome",
281            "status": "preview",
282            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
283        },
284        {
285            "@id": "/measurement-sets/IGVFDS3622WNKQ/",
286            "accession": "IGVFDS3622WNKQ",
287            "aliases": [
288                "igvf:corces_measurementSet_RP013_G2_ATAC"
289            ],
290            "file_set_type": "experimental data",
291            "lab": {
292                "title": "Ryan Corces, Gladstone Institute UCSF"
293            },
294            "preferred_assay_title": "10x multiome",
295            "status": "preview",
296            "summary": "single-nucleus ATAC-seq (10x multiome)"
297        },
298        {
299            "@id": "/measurement-sets/IGVFDS7473ITUN/",
300            "accession": "IGVFDS7473ITUN",
301            "aliases": [
302                "igvf:corces_measurementSet_RP013_G2_RNA"
303            ],
304            "file_set_type": "experimental data",
305            "lab": {
306                "title": "Ryan Corces, Gladstone Institute UCSF"
307            },
308            "preferred_assay_title": "10x multiome",
309            "status": "preview",
310            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
311        },
312        {
313            "@id": "/measurement-sets/IGVFDS2391MEXB/",
314            "accession": "IGVFDS2391MEXB",
315            "aliases": [
316                "igvf:corces_measurementSet_RP013_G3_ATAC"
317            ],
318            "file_set_type": "experimental data",
319            "lab": {
320                "title": "Ryan Corces, Gladstone Institute UCSF"
321            },
322            "preferred_assay_title": "10x multiome",
323            "status": "preview",
324            "summary": "single-nucleus ATAC-seq (10x multiome)"
325        },
326        {
327            "@id": "/measurement-sets/IGVFDS4413FCPJ/",
328            "accession": "IGVFDS4413FCPJ",
329            "aliases": [
330                "igvf:corces_measurementSet_RP013_G3_RNA"
331            ],
332            "file_set_type": "experimental data",
333            "lab": {
334                "title": "Ryan Corces, Gladstone Institute UCSF"
335            },
336            "preferred_assay_title": "10x multiome",
337            "status": "preview",
338            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
339        },
340        {
341            "@id": "/measurement-sets/IGVFDS7055SHHA/",
342            "accession": "IGVFDS7055SHHA",
343            "aliases": [
344                "igvf:corces_measurementSet_RP013_G8_ATAC"
345            ],
346            "file_set_type": "experimental data",
347            "lab": {
348                "title": "Ryan Corces, Gladstone Institute UCSF"
349            },
350            "preferred_assay_title": "10x multiome",
351            "status": "preview",
352            "summary": "single-nucleus ATAC-seq (10x multiome)"
353        },
354        {
355            "@id": "/measurement-sets/IGVFDS6105WUJZ/",
356            "accession": "IGVFDS6105WUJZ",
357            "aliases": [
358                "igvf:corces_measurementSet_RP013_G8_RNA"
359            ],
360            "file_set_type": "experimental data",
361            "lab": {
362                "title": "Ryan Corces, Gladstone Institute UCSF"
363            },
364            "preferred_assay_title": "10x multiome",
365            "status": "preview",
366            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
367        },
368        {
369            "@id": "/measurement-sets/IGVFDS2373GWYA/",
370            "accession": "IGVFDS2373GWYA",
371            "aliases": [
372                "igvf:corces_measurementSet_RP013_G1_ATAC"
373            ],
374            "file_set_type": "experimental data",
375            "lab": {
376                "title": "Ryan Corces, Gladstone Institute UCSF"
377            },
378            "preferred_assay_title": "10x multiome",
379            "status": "preview",
380            "summary": "single-nucleus ATAC-seq (10x multiome)"
381        },
382        {
383            "@id": "/measurement-sets/IGVFDS8759JYNP/",
384            "accession": "IGVFDS8759JYNP",
385            "aliases": [
386                "igvf:corces_measurementSet_RP013_G1_RNA"
387            ],
388            "file_set_type": "experimental data",
389            "lab": {
390                "title": "Ryan Corces, Gladstone Institute UCSF"
391            },
392            "preferred_assay_title": "10x multiome",
393            "status": "preview",
394            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
395        },
396        {
397            "@id": "/measurement-sets/IGVFDS3109FOBL/",
398            "accession": "IGVFDS3109FOBL",
399            "aliases": [
400                "igvf:corces_measurementSet_RP013_G4_ATAC"
401            ],
402            "file_set_type": "experimental data",
403            "lab": {
404                "title": "Ryan Corces, Gladstone Institute UCSF"
405            },
406            "preferred_assay_title": "10x multiome",
407            "status": "preview",
408            "summary": "single-nucleus ATAC-seq (10x multiome)"
409        },
410        {
411            "@id": "/measurement-sets/IGVFDS6915EFKE/",
412            "accession": "IGVFDS6915EFKE",
413            "aliases": [
414                "igvf:corces_measurementSet_RP013_G4_RNA"
415            ],
416            "file_set_type": "experimental data",
417            "lab": {
418                "title": "Ryan Corces, Gladstone Institute UCSF"
419            },
420            "preferred_assay_title": "10x multiome",
421            "status": "preview",
422            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
423        },
424        {
425            "@id": "/measurement-sets/IGVFDS0028AWOA/",
426            "accession": "IGVFDS0028AWOA",
427            "aliases": [
428                "igvf:corces_measurementSet_RP013_G7_ATAC"
429            ],
430            "file_set_type": "experimental data",
431            "lab": {
432                "title": "Ryan Corces, Gladstone Institute UCSF"
433            },
434            "preferred_assay_title": "10x multiome",
435            "status": "preview",
436            "summary": "single-nucleus ATAC-seq (10x multiome)"
437        },
438        {
439            "@id": "/measurement-sets/IGVFDS5571RDTA/",
440            "accession": "IGVFDS5571RDTA",
441            "aliases": [
442                "igvf:corces_measurementSet_RP013_G7_RNA"
443            ],
444            "file_set_type": "experimental data",
445            "lab": {
446                "title": "Ryan Corces, Gladstone Institute UCSF"
447            },
448            "preferred_assay_title": "10x multiome",
449            "status": "preview",
450            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
451        },
452        {
453            "@id": "/measurement-sets/IGVFDS0088WTOH/",
454            "accession": "IGVFDS0088WTOH",
455            "aliases": [
456                "igvf:corces_measurementSet_RP013_G5_ATAC"
457            ],
458            "file_set_type": "experimental data",
459            "lab": {
460                "title": "Ryan Corces, Gladstone Institute UCSF"
461            },
462            "preferred_assay_title": "10x multiome",
463            "status": "preview",
464            "summary": "single-nucleus ATAC-seq (10x multiome)"
465        },
466        {
467            "@id": "/measurement-sets/IGVFDS9639FMLS/",
468            "accession": "IGVFDS9639FMLS",
469            "aliases": [
470                "igvf:corces_measurementSet_RP013_G5_RNA"
471            ],
472            "file_set_type": "experimental data",
473            "lab": {
474                "title": "Ryan Corces, Gladstone Institute UCSF"
475            },
476            "preferred_assay_title": "10x multiome",
477            "status": "preview",
478            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
479        },
480        {
481            "@id": "/measurement-sets/IGVFDS5114LZUX/",
482            "accession": "IGVFDS5114LZUX",
483            "aliases": [
484                "igvf:corces_measurementSet_RP013_G6_ATAC"
485            ],
486            "file_set_type": "experimental data",
487            "lab": {
488                "title": "Ryan Corces, Gladstone Institute UCSF"
489            },
490            "preferred_assay_title": "10x multiome",
491            "status": "preview",
492            "summary": "single-nucleus ATAC-seq (10x multiome)"
493        },
494        {
495            "@id": "/measurement-sets/IGVFDS5127RSAZ/",
496            "accession": "IGVFDS5127RSAZ",
497            "aliases": [
498                "igvf:corces_measurementSet_RP013_G6_RNA"
499            ],
500            "file_set_type": "experimental data",
501            "lab": {
502                "title": "Ryan Corces, Gladstone Institute UCSF"
503            },
504            "preferred_assay_title": "10x multiome",
505            "status": "preview",
506            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
507        }
508    ],
509    "institutional_certificates": [
510        {
511            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
512            "certificate_identifier": "IP115-05",
513            "controlled_access": false,
514            "status": "in progress"
515        }
516    ],
517    "lab": {
518        "@id": "/labs/ryan-corces/",
519        "title": "Ryan Corces, Gladstone Institute UCSF"
520    },
521    "lower_bound_age": 72,
522    "lower_bound_age_in_hours": 630720,
523    "multiplexed_in": [
524        {
525            "@id": "/multiplexed-samples/IGVFSM2480DKQY/",
526            "accession": "IGVFSM2480DKQY",
527            "status": "preview"
528        },
529        {
530            "@id": "/multiplexed-samples/IGVFSM1132ELYG/",
531            "accession": "IGVFSM1132ELYG",
532            "status": "preview"
533        },
534        {
535            "@id": "/multiplexed-samples/IGVFSM3739CWYU/",
536            "accession": "IGVFSM3739CWYU",
537            "status": "preview"
538        },
539        {
540            "@id": "/multiplexed-samples/IGVFSM6255JGZM/",
541            "accession": "IGVFSM6255JGZM",
542            "status": "preview"
543        },
544        {
545            "@id": "/multiplexed-samples/IGVFSM1167MABH/",
546            "accession": "IGVFSM1167MABH",
547            "status": "preview"
548        },
549        {
550            "@id": "/multiplexed-samples/IGVFSM2293QQTO/",
551            "accession": "IGVFSM2293QQTO",
552            "status": "preview"
553        },
554        {
555            "@id": "/multiplexed-samples/IGVFSM8971IRDZ/",
556            "accession": "IGVFSM8971IRDZ",
557            "status": "preview"
558        },
559        {
560            "@id": "/multiplexed-samples/IGVFSM9775XYEX/",
561            "accession": "IGVFSM9775XYEX",
562            "status": "preview"
563        },
564        {
565            "@id": "/multiplexed-samples/IGVFSM5080SUXQ/",
566            "accession": "IGVFSM5080SUXQ",
567            "status": "preview"
568        },
569        {
570            "@id": "/multiplexed-samples/IGVFSM2861OAVH/",
571            "accession": "IGVFSM2861OAVH",
572            "status": "preview"
573        },
574        {
575            "@id": "/multiplexed-samples/IGVFSM7640TBFV/",
576            "accession": "IGVFSM7640TBFV",
577            "status": "preview"
578        },
579        {
580            "@id": "/multiplexed-samples/IGVFSM3819ZCMN/",
581            "accession": "IGVFSM3819ZCMN",
582            "status": "preview"
583        },
584        {
585            "@id": "/multiplexed-samples/IGVFSM1576QCMO/",
586            "accession": "IGVFSM1576QCMO",
587            "status": "preview"
588        },
589        {
590            "@id": "/multiplexed-samples/IGVFSM7012MRMQ/",
591            "accession": "IGVFSM7012MRMQ",
592            "status": "preview"
593        },
594        {
595            "@id": "/multiplexed-samples/IGVFSM8342TFWF/",
596            "accession": "IGVFSM8342TFWF",
597            "status": "preview"
598        },
599        {
600            "@id": "/multiplexed-samples/IGVFSM6292QYDO/",
601            "accession": "IGVFSM6292QYDO",
602            "status": "preview"
603        }
604    ],
605    "origin_of": [],
606    "parts": [],
607    "pmi": 276,
608    "pmi_units": "minute",
609    "pooled_in": [],
610    "preservation_method": "flash-freezing",
611    "protocols": [
612        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
613    ],
614    "sample_terms": [
615        {
616            "@id": "/sample-terms/UBERON_0002038/",
617            "status": "preview",
618            "term_name": "substantia nigra"
619        }
620    ],
621    "schema_version": "21",
622    "sex": "male",
623    "sorted_fractions": [],
624    "sources": [
625        {
626            "@id": "/sources/banner-health/",
627            "status": "released",
628            "title": "Banner Health"
629        }
630    ],
631    "status": "preview",
632    "submitted_by": {
633        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
634        "title": "Ryan Corces"
635    },
636    "summary": "Homo sapiens (male, 72 years) substantia nigra tissue associated with cerebral amyloid angiopathy",
637    "taxa": "Homo sapiens",
638    "upper_bound_age": 72,
639    "upper_bound_age_in_hours": 630720,
640    "uuid": "b85375d6-7662-47fc-bae1-5458e6436435",
641    "virtual": false
642}