substantia nigra — IGVFSM3348GEXC

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM3348GEXC/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM3348GEXC",
11    "age": "79",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN0002_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM3348GEXC](/tissues/IGVFSM3348GEXC/) 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/IGVFSM3348GEXC/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM3348GEXC](/tissues/IGVFSM3348GEXC/) 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/IGVFSM3348GEXC/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:12:36.665330+00:00",
44    "date_obtained": "2023-02-01",
45    "disease_terms": [
46        {
47            "@id": "/phenotype-terms/MONDO_0004975/",
48            "status": "released",
49            "term_name": "Alzheimer disease"
50        },
51        {
52            "@id": "/phenotype-terms/DOID_14330/",
53            "status": "in progress",
54            "term_name": "Parkinson's disease"
55        }
56    ],
57    "donors": [
58        {
59            "@id": "/human-donors/IGVFDO3497MBPK/",
60            "accession": "IGVFDO3497MBPK",
61            "ethnicities": [
62                "European"
63            ],
64            "status": "preview"
65        }
66    ],
67    "file_sets": [
68        {
69            "@id": "/measurement-sets/IGVFDS2132XMHB/",
70            "accession": "IGVFDS2132XMHB",
71            "aliases": [
72                "igvf:corces_measurementSet_X032_G4_ATAC"
73            ],
74            "file_set_type": "experimental data",
75            "lab": {
76                "title": "Ryan Corces, Gladstone Institute UCSF"
77            },
78            "preferred_assay_title": "10x multiome",
79            "status": "preview",
80            "summary": "single-nucleus ATAC-seq (10x multiome)"
81        },
82        {
83            "@id": "/measurement-sets/IGVFDS3071WPNU/",
84            "accession": "IGVFDS3071WPNU",
85            "aliases": [
86                "igvf:corces_measurementSet_X032_G4_RNA"
87            ],
88            "file_set_type": "experimental data",
89            "lab": {
90                "title": "Ryan Corces, Gladstone Institute UCSF"
91            },
92            "preferred_assay_title": "10x multiome",
93            "status": "preview",
94            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
95        },
96        {
97            "@id": "/measurement-sets/IGVFDS2336BWET/",
98            "accession": "IGVFDS2336BWET",
99            "aliases": [
100                "igvf:corces_measurementSet_X032_G8_ATAC"
101            ],
102            "file_set_type": "experimental data",
103            "lab": {
104                "title": "Ryan Corces, Gladstone Institute UCSF"
105            },
106            "preferred_assay_title": "10x multiome",
107            "status": "preview",
108            "summary": "single-nucleus ATAC-seq (10x multiome)"
109        },
110        {
111            "@id": "/measurement-sets/IGVFDS7019JXXD/",
112            "accession": "IGVFDS7019JXXD",
113            "aliases": [
114                "igvf:corces_measurementSet_X032_G8_RNA"
115            ],
116            "file_set_type": "experimental data",
117            "lab": {
118                "title": "Ryan Corces, Gladstone Institute UCSF"
119            },
120            "preferred_assay_title": "10x multiome",
121            "status": "preview",
122            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
123        },
124        {
125            "@id": "/measurement-sets/IGVFDS3080TIMY/",
126            "accession": "IGVFDS3080TIMY",
127            "aliases": [
128                "igvf:corces_measurementSet_X032_G1_ATAC"
129            ],
130            "file_set_type": "experimental data",
131            "lab": {
132                "title": "Ryan Corces, Gladstone Institute UCSF"
133            },
134            "preferred_assay_title": "10x multiome",
135            "status": "preview",
136            "summary": "single-nucleus ATAC-seq (10x multiome)"
137        },
138        {
139            "@id": "/measurement-sets/IGVFDS3535IMWQ/",
140            "accession": "IGVFDS3535IMWQ",
141            "aliases": [
142                "igvf:corces_measurementSet_X032_G1_RNA"
143            ],
144            "file_set_type": "experimental data",
145            "lab": {
146                "title": "Ryan Corces, Gladstone Institute UCSF"
147            },
148            "preferred_assay_title": "10x multiome",
149            "status": "preview",
150            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
151        },
152        {
153            "@id": "/measurement-sets/IGVFDS4088CJJR/",
154            "accession": "IGVFDS4088CJJR",
155            "aliases": [
156                "igvf:corces_measurementSet_X032_G7_ATAC"
157            ],
158            "file_set_type": "experimental data",
159            "lab": {
160                "title": "Ryan Corces, Gladstone Institute UCSF"
161            },
162            "preferred_assay_title": "10x multiome",
163            "status": "preview",
164            "summary": "single-nucleus ATAC-seq (10x multiome)"
165        },
166        {
167            "@id": "/measurement-sets/IGVFDS7706LHLI/",
168            "accession": "IGVFDS7706LHLI",
169            "aliases": [
170                "igvf:corces_measurementSet_X032_G7_RNA"
171            ],
172            "file_set_type": "experimental data",
173            "lab": {
174                "title": "Ryan Corces, Gladstone Institute UCSF"
175            },
176            "preferred_assay_title": "10x multiome",
177            "status": "preview",
178            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
179        },
180        {
181            "@id": "/measurement-sets/IGVFDS7833BTPG/",
182            "accession": "IGVFDS7833BTPG",
183            "aliases": [
184                "igvf:corces_measurementSet_X032_G3_ATAC"
185            ],
186            "file_set_type": "experimental data",
187            "lab": {
188                "title": "Ryan Corces, Gladstone Institute UCSF"
189            },
190            "preferred_assay_title": "10x multiome",
191            "status": "preview",
192            "summary": "single-nucleus ATAC-seq (10x multiome)"
193        },
194        {
195            "@id": "/measurement-sets/IGVFDS9057KJEI/",
196            "accession": "IGVFDS9057KJEI",
197            "aliases": [
198                "igvf:corces_measurementSet_X032_G3_RNA"
199            ],
200            "file_set_type": "experimental data",
201            "lab": {
202                "title": "Ryan Corces, Gladstone Institute UCSF"
203            },
204            "preferred_assay_title": "10x multiome",
205            "status": "preview",
206            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
207        },
208        {
209            "@id": "/measurement-sets/IGVFDS6899OQTS/",
210            "accession": "IGVFDS6899OQTS",
211            "aliases": [
212                "igvf:corces_measurementSet_X032_G2_ATAC"
213            ],
214            "file_set_type": "experimental data",
215            "lab": {
216                "title": "Ryan Corces, Gladstone Institute UCSF"
217            },
218            "preferred_assay_title": "10x multiome",
219            "status": "preview",
220            "summary": "single-nucleus ATAC-seq (10x multiome)"
221        },
222        {
223            "@id": "/measurement-sets/IGVFDS0346MQLV/",
224            "accession": "IGVFDS0346MQLV",
225            "aliases": [
226                "igvf:corces_measurementSet_X032_G2_RNA"
227            ],
228            "file_set_type": "experimental data",
229            "lab": {
230                "title": "Ryan Corces, Gladstone Institute UCSF"
231            },
232            "preferred_assay_title": "10x multiome",
233            "status": "preview",
234            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
235        },
236        {
237            "@id": "/measurement-sets/IGVFDS5776BDPL/",
238            "accession": "IGVFDS5776BDPL",
239            "aliases": [
240                "igvf:corces_measurementSet_X032_G5_ATAC"
241            ],
242            "file_set_type": "experimental data",
243            "lab": {
244                "title": "Ryan Corces, Gladstone Institute UCSF"
245            },
246            "preferred_assay_title": "10x multiome",
247            "status": "preview",
248            "summary": "single-nucleus ATAC-seq (10x multiome)"
249        },
250        {
251            "@id": "/measurement-sets/IGVFDS6220QSDQ/",
252            "accession": "IGVFDS6220QSDQ",
253            "aliases": [
254                "igvf:corces_measurementSet_X032_G5_RNA"
255            ],
256            "file_set_type": "experimental data",
257            "lab": {
258                "title": "Ryan Corces, Gladstone Institute UCSF"
259            },
260            "preferred_assay_title": "10x multiome",
261            "status": "preview",
262            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
263        },
264        {
265            "@id": "/measurement-sets/IGVFDS2723SVTT/",
266            "accession": "IGVFDS2723SVTT",
267            "aliases": [
268                "igvf:corces_measurementSet_X032_G6_ATAC"
269            ],
270            "file_set_type": "experimental data",
271            "lab": {
272                "title": "Ryan Corces, Gladstone Institute UCSF"
273            },
274            "preferred_assay_title": "10x multiome",
275            "status": "preview",
276            "summary": "single-nucleus ATAC-seq (10x multiome)"
277        },
278        {
279            "@id": "/measurement-sets/IGVFDS5452ZVED/",
280            "accession": "IGVFDS5452ZVED",
281            "aliases": [
282                "igvf:corces_measurementSet_X032_G6_RNA"
283            ],
284            "file_set_type": "experimental data",
285            "lab": {
286                "title": "Ryan Corces, Gladstone Institute UCSF"
287            },
288            "preferred_assay_title": "10x multiome",
289            "status": "preview",
290            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
291        },
292        {
293            "@id": "/measurement-sets/IGVFDS5362QJCF/",
294            "accession": "IGVFDS5362QJCF",
295            "aliases": [
296                "igvf:corces_measurementSet_RP011_G3_ATAC"
297            ],
298            "file_set_type": "experimental data",
299            "lab": {
300                "title": "Ryan Corces, Gladstone Institute UCSF"
301            },
302            "preferred_assay_title": "10x multiome",
303            "status": "preview",
304            "summary": "single-nucleus ATAC-seq (10x multiome)"
305        },
306        {
307            "@id": "/measurement-sets/IGVFDS1279DJVE/",
308            "accession": "IGVFDS1279DJVE",
309            "aliases": [
310                "igvf:corces_measurementSet_RP011_G3_RNA"
311            ],
312            "file_set_type": "experimental data",
313            "lab": {
314                "title": "Ryan Corces, Gladstone Institute UCSF"
315            },
316            "preferred_assay_title": "10x multiome",
317            "status": "preview",
318            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
319        },
320        {
321            "@id": "/measurement-sets/IGVFDS0856IUPF/",
322            "accession": "IGVFDS0856IUPF",
323            "aliases": [
324                "igvf:corces_measurementSet_RP011_G6_ATAC"
325            ],
326            "file_set_type": "experimental data",
327            "lab": {
328                "title": "Ryan Corces, Gladstone Institute UCSF"
329            },
330            "preferred_assay_title": "10x multiome",
331            "status": "preview",
332            "summary": "single-nucleus ATAC-seq (10x multiome)"
333        },
334        {
335            "@id": "/measurement-sets/IGVFDS8611TPMB/",
336            "accession": "IGVFDS8611TPMB",
337            "aliases": [
338                "igvf:corces_measurementSet_RP011_G6_RNA"
339            ],
340            "file_set_type": "experimental data",
341            "lab": {
342                "title": "Ryan Corces, Gladstone Institute UCSF"
343            },
344            "preferred_assay_title": "10x multiome",
345            "status": "preview",
346            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
347        },
348        {
349            "@id": "/measurement-sets/IGVFDS3484DNVB/",
350            "accession": "IGVFDS3484DNVB",
351            "aliases": [
352                "igvf:corces_measurementSet_RP011_G5_RNA"
353            ],
354            "file_set_type": "experimental data",
355            "lab": {
356                "title": "Ryan Corces, Gladstone Institute UCSF"
357            },
358            "preferred_assay_title": "10x multiome",
359            "status": "preview",
360            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
361        },
362        {
363            "@id": "/measurement-sets/IGVFDS3602NEYS/",
364            "accession": "IGVFDS3602NEYS",
365            "aliases": [
366                "igvf:corces_measurementSet_RP011_G5_ATAC"
367            ],
368            "file_set_type": "experimental data",
369            "lab": {
370                "title": "Ryan Corces, Gladstone Institute UCSF"
371            },
372            "preferred_assay_title": "10x multiome",
373            "status": "preview",
374            "summary": "single-nucleus ATAC-seq (10x multiome)"
375        },
376        {
377            "@id": "/measurement-sets/IGVFDS5146PTIC/",
378            "accession": "IGVFDS5146PTIC",
379            "aliases": [
380                "igvf:corces_measurementSet_RP011_G7_ATAC"
381            ],
382            "file_set_type": "experimental data",
383            "lab": {
384                "title": "Ryan Corces, Gladstone Institute UCSF"
385            },
386            "preferred_assay_title": "10x multiome",
387            "status": "preview",
388            "summary": "single-nucleus ATAC-seq (10x multiome)"
389        },
390        {
391            "@id": "/measurement-sets/IGVFDS2300TLPU/",
392            "accession": "IGVFDS2300TLPU",
393            "aliases": [
394                "igvf:corces_measurementSet_RP011_G7_RNA"
395            ],
396            "file_set_type": "experimental data",
397            "lab": {
398                "title": "Ryan Corces, Gladstone Institute UCSF"
399            },
400            "preferred_assay_title": "10x multiome",
401            "status": "preview",
402            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
403        },
404        {
405            "@id": "/measurement-sets/IGVFDS2229EHIM/",
406            "accession": "IGVFDS2229EHIM",
407            "aliases": [
408                "igvf:corces_measurementSet_RP011_G1_ATAC"
409            ],
410            "file_set_type": "experimental data",
411            "lab": {
412                "title": "Ryan Corces, Gladstone Institute UCSF"
413            },
414            "preferred_assay_title": "10x multiome",
415            "status": "preview",
416            "summary": "single-nucleus ATAC-seq (10x multiome)"
417        },
418        {
419            "@id": "/measurement-sets/IGVFDS3628MXUK/",
420            "accession": "IGVFDS3628MXUK",
421            "aliases": [
422                "igvf:corces_measurementSet_RP011_G1_RNA"
423            ],
424            "file_set_type": "experimental data",
425            "lab": {
426                "title": "Ryan Corces, Gladstone Institute UCSF"
427            },
428            "preferred_assay_title": "10x multiome",
429            "status": "preview",
430            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
431        },
432        {
433            "@id": "/measurement-sets/IGVFDS0831CAYJ/",
434            "accession": "IGVFDS0831CAYJ",
435            "aliases": [
436                "igvf:corces_measurementSet_RP011_G4_ATAC"
437            ],
438            "file_set_type": "experimental data",
439            "lab": {
440                "title": "Ryan Corces, Gladstone Institute UCSF"
441            },
442            "preferred_assay_title": "10x multiome",
443            "status": "preview",
444            "summary": "single-nucleus ATAC-seq (10x multiome)"
445        },
446        {
447            "@id": "/measurement-sets/IGVFDS4334WKOE/",
448            "accession": "IGVFDS4334WKOE",
449            "aliases": [
450                "igvf:corces_measurementSet_RP011_G4_RNA"
451            ],
452            "file_set_type": "experimental data",
453            "lab": {
454                "title": "Ryan Corces, Gladstone Institute UCSF"
455            },
456            "preferred_assay_title": "10x multiome",
457            "status": "preview",
458            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
459        },
460        {
461            "@id": "/measurement-sets/IGVFDS8666KHZN/",
462            "accession": "IGVFDS8666KHZN",
463            "aliases": [
464                "igvf:corces_measurementSet_RP011_G2_ATAC"
465            ],
466            "file_set_type": "experimental data",
467            "lab": {
468                "title": "Ryan Corces, Gladstone Institute UCSF"
469            },
470            "preferred_assay_title": "10x multiome",
471            "status": "preview",
472            "summary": "single-nucleus ATAC-seq (10x multiome)"
473        },
474        {
475            "@id": "/measurement-sets/IGVFDS7806UOQI/",
476            "accession": "IGVFDS7806UOQI",
477            "aliases": [
478                "igvf:corces_measurementSet_RP011_G2_RNA"
479            ],
480            "file_set_type": "experimental data",
481            "lab": {
482                "title": "Ryan Corces, Gladstone Institute UCSF"
483            },
484            "preferred_assay_title": "10x multiome",
485            "status": "preview",
486            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
487        },
488        {
489            "@id": "/measurement-sets/IGVFDS3035QFKU/",
490            "accession": "IGVFDS3035QFKU",
491            "aliases": [
492                "igvf:corces_measurementSet_RP011_G8_ATAC"
493            ],
494            "file_set_type": "experimental data",
495            "lab": {
496                "title": "Ryan Corces, Gladstone Institute UCSF"
497            },
498            "preferred_assay_title": "10x multiome",
499            "status": "preview",
500            "summary": "single-nucleus ATAC-seq (10x multiome)"
501        },
502        {
503            "@id": "/measurement-sets/IGVFDS6373YBDI/",
504            "accession": "IGVFDS6373YBDI",
505            "aliases": [
506                "igvf:corces_measurementSet_RP011_G8_RNA"
507            ],
508            "file_set_type": "experimental data",
509            "lab": {
510                "title": "Ryan Corces, Gladstone Institute UCSF"
511            },
512            "preferred_assay_title": "10x multiome",
513            "status": "preview",
514            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
515        }
516    ],
517    "institutional_certificates": [
518        {
519            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
520            "certificate_identifier": "IP115-05",
521            "controlled_access": false,
522            "status": "in progress"
523        }
524    ],
525    "lab": {
526        "@id": "/labs/ryan-corces/",
527        "title": "Ryan Corces, Gladstone Institute UCSF"
528    },
529    "lower_bound_age": 79,
530    "lower_bound_age_in_hours": 692040,
531    "multiplexed_in": [
532        {
533            "@id": "/multiplexed-samples/IGVFSM5595EQCW/",
534            "accession": "IGVFSM5595EQCW",
535            "status": "preview"
536        },
537        {
538            "@id": "/multiplexed-samples/IGVFSM8574LYFF/",
539            "accession": "IGVFSM8574LYFF",
540            "status": "preview"
541        },
542        {
543            "@id": "/multiplexed-samples/IGVFSM6835GLQE/",
544            "accession": "IGVFSM6835GLQE",
545            "status": "preview"
546        },
547        {
548            "@id": "/multiplexed-samples/IGVFSM2646IJIB/",
549            "accession": "IGVFSM2646IJIB",
550            "status": "preview"
551        },
552        {
553            "@id": "/multiplexed-samples/IGVFSM7956ZXDL/",
554            "accession": "IGVFSM7956ZXDL",
555            "status": "preview"
556        },
557        {
558            "@id": "/multiplexed-samples/IGVFSM8298WTCX/",
559            "accession": "IGVFSM8298WTCX",
560            "status": "preview"
561        },
562        {
563            "@id": "/multiplexed-samples/IGVFSM8487OHPZ/",
564            "accession": "IGVFSM8487OHPZ",
565            "status": "preview"
566        },
567        {
568            "@id": "/multiplexed-samples/IGVFSM8028VLKJ/",
569            "accession": "IGVFSM8028VLKJ",
570            "status": "preview"
571        },
572        {
573            "@id": "/multiplexed-samples/IGVFSM0695RJYV/",
574            "accession": "IGVFSM0695RJYV",
575            "status": "preview"
576        },
577        {
578            "@id": "/multiplexed-samples/IGVFSM6926MVZN/",
579            "accession": "IGVFSM6926MVZN",
580            "status": "preview"
581        },
582        {
583            "@id": "/multiplexed-samples/IGVFSM0643EUKR/",
584            "accession": "IGVFSM0643EUKR",
585            "status": "preview"
586        },
587        {
588            "@id": "/multiplexed-samples/IGVFSM5471WRIH/",
589            "accession": "IGVFSM5471WRIH",
590            "status": "preview"
591        },
592        {
593            "@id": "/multiplexed-samples/IGVFSM4137SEKT/",
594            "accession": "IGVFSM4137SEKT",
595            "status": "preview"
596        },
597        {
598            "@id": "/multiplexed-samples/IGVFSM9332LJBD/",
599            "accession": "IGVFSM9332LJBD",
600            "status": "preview"
601        },
602        {
603            "@id": "/multiplexed-samples/IGVFSM9347ZBKI/",
604            "accession": "IGVFSM9347ZBKI",
605            "status": "preview"
606        },
607        {
608            "@id": "/multiplexed-samples/IGVFSM3747QRCH/",
609            "accession": "IGVFSM3747QRCH",
610            "status": "preview"
611        }
612    ],
613    "origin_of": [],
614    "parts": [],
615    "pmi": 180,
616    "pmi_units": "minute",
617    "pooled_in": [],
618    "preservation_method": "flash-freezing",
619    "protocols": [
620        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
621    ],
622    "sample_terms": [
623        {
624            "@id": "/sample-terms/UBERON_0002038/",
625            "status": "preview",
626            "term_name": "substantia nigra"
627        }
628    ],
629    "schema_version": "21",
630    "sex": "male",
631    "sorted_fractions": [],
632    "sources": [
633        {
634            "@id": "/sources/banner-health/",
635            "status": "released",
636            "title": "Banner Health"
637        }
638    ],
639    "status": "preview",
640    "submitted_by": {
641        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
642        "title": "Ryan Corces"
643    },
644    "summary": "Homo sapiens (male, 79 years) substantia nigra tissue associated with Alzheimer disease, Parkinson's disease",
645    "taxa": "Homo sapiens",
646    "upper_bound_age": 79,
647    "upper_bound_age_in_hours": 692040,
648    "uuid": "f4a030be-dbd1-47e6-8638-4b16644de63e",
649    "virtual": false
650}