substantia nigra — IGVFSM0789BXPQ

1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM0789BXPQ/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM0789BXPQ",
11    "age": "89",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN0341_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "missing CCF ID",
20                "detail": "Tissue [IGVFSM0789BXPQ](/tissues/IGVFSM0789BXPQ/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_tissue_ccf_id",
24                "path": "/tissues/IGVFSM0789BXPQ/"
25            }
26        ]
27    },
28    "award": {
29        "@id": "/awards/HG012076/",
30        "component": "mapping"
31    },
32    "classifications": [
33        "tissue"
34    ],
35    "creation_timestamp": "2025-03-19T04:13:14.406358+00:00",
36    "date_obtained": "2023-02-13",
37    "donors": [
38        {
39            "@id": "/human-donors/IGVFDO7754VJKM/",
40            "accession": "IGVFDO7754VJKM",
41            "ethnicities": [
42                "European"
43            ],
44            "status": "preview"
45        }
46    ],
47    "file_sets": [
48        {
49            "@id": "/measurement-sets/IGVFDS7439FTUN/",
50            "accession": "IGVFDS7439FTUN",
51            "aliases": [
52                "igvf:corces_measurementSet_X035_G7_ATAC"
53            ],
54            "file_set_type": "experimental data",
55            "lab": {
56                "title": "Ryan Corces, Gladstone Institute UCSF"
57            },
58            "preferred_assay_title": "10x multiome",
59            "status": "preview",
60            "summary": "single-nucleus ATAC-seq (10x multiome)"
61        },
62        {
63            "@id": "/measurement-sets/IGVFDS1448IDZP/",
64            "accession": "IGVFDS1448IDZP",
65            "aliases": [
66                "igvf:corces_measurementSet_X035_G7_RNA"
67            ],
68            "file_set_type": "experimental data",
69            "lab": {
70                "title": "Ryan Corces, Gladstone Institute UCSF"
71            },
72            "preferred_assay_title": "10x multiome",
73            "status": "preview",
74            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
75        },
76        {
77            "@id": "/measurement-sets/IGVFDS6760HDFY/",
78            "accession": "IGVFDS6760HDFY",
79            "aliases": [
80                "igvf:corces_measurementSet_X035_G5_ATAC"
81            ],
82            "file_set_type": "experimental data",
83            "lab": {
84                "title": "Ryan Corces, Gladstone Institute UCSF"
85            },
86            "preferred_assay_title": "10x multiome",
87            "status": "preview",
88            "summary": "single-nucleus ATAC-seq (10x multiome)"
89        },
90        {
91            "@id": "/measurement-sets/IGVFDS4916WYYZ/",
92            "accession": "IGVFDS4916WYYZ",
93            "aliases": [
94                "igvf:corces_measurementSet_X035_G5_RNA"
95            ],
96            "file_set_type": "experimental data",
97            "lab": {
98                "title": "Ryan Corces, Gladstone Institute UCSF"
99            },
100            "preferred_assay_title": "10x multiome",
101            "status": "preview",
102            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
103        },
104        {
105            "@id": "/measurement-sets/IGVFDS0111NTYK/",
106            "accession": "IGVFDS0111NTYK",
107            "aliases": [
108                "igvf:corces_measurementSet_X035_G1_ATAC"
109            ],
110            "file_set_type": "experimental data",
111            "lab": {
112                "title": "Ryan Corces, Gladstone Institute UCSF"
113            },
114            "preferred_assay_title": "10x multiome",
115            "status": "preview",
116            "summary": "single-nucleus ATAC-seq (10x multiome)"
117        },
118        {
119            "@id": "/measurement-sets/IGVFDS9194EJGS/",
120            "accession": "IGVFDS9194EJGS",
121            "aliases": [
122                "igvf:corces_measurementSet_X035_G1_RNA"
123            ],
124            "file_set_type": "experimental data",
125            "lab": {
126                "title": "Ryan Corces, Gladstone Institute UCSF"
127            },
128            "preferred_assay_title": "10x multiome",
129            "status": "preview",
130            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
131        },
132        {
133            "@id": "/measurement-sets/IGVFDS4325THSS/",
134            "accession": "IGVFDS4325THSS",
135            "aliases": [
136                "igvf:corces_measurementSet_X035_G2_ATAC"
137            ],
138            "file_set_type": "experimental data",
139            "lab": {
140                "title": "Ryan Corces, Gladstone Institute UCSF"
141            },
142            "preferred_assay_title": "10x multiome",
143            "status": "preview",
144            "summary": "single-nucleus ATAC-seq (10x multiome)"
145        },
146        {
147            "@id": "/measurement-sets/IGVFDS8073HHQK/",
148            "accession": "IGVFDS8073HHQK",
149            "aliases": [
150                "igvf:corces_measurementSet_X035_G2_RNA"
151            ],
152            "file_set_type": "experimental data",
153            "lab": {
154                "title": "Ryan Corces, Gladstone Institute UCSF"
155            },
156            "preferred_assay_title": "10x multiome",
157            "status": "preview",
158            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
159        },
160        {
161            "@id": "/measurement-sets/IGVFDS1848DGUM/",
162            "accession": "IGVFDS1848DGUM",
163            "aliases": [
164                "igvf:corces_measurementSet_X035_G4_ATAC"
165            ],
166            "file_set_type": "experimental data",
167            "lab": {
168                "title": "Ryan Corces, Gladstone Institute UCSF"
169            },
170            "preferred_assay_title": "10x multiome",
171            "status": "preview",
172            "summary": "single-nucleus ATAC-seq (10x multiome)"
173        },
174        {
175            "@id": "/measurement-sets/IGVFDS7152NKCN/",
176            "accession": "IGVFDS7152NKCN",
177            "aliases": [
178                "igvf:corces_measurementSet_X035_G4_RNA"
179            ],
180            "file_set_type": "experimental data",
181            "lab": {
182                "title": "Ryan Corces, Gladstone Institute UCSF"
183            },
184            "preferred_assay_title": "10x multiome",
185            "status": "preview",
186            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
187        },
188        {
189            "@id": "/measurement-sets/IGVFDS3392QGFY/",
190            "accession": "IGVFDS3392QGFY",
191            "aliases": [
192                "igvf:corces_measurementSet_X035_G6_ATAC"
193            ],
194            "file_set_type": "experimental data",
195            "lab": {
196                "title": "Ryan Corces, Gladstone Institute UCSF"
197            },
198            "preferred_assay_title": "10x multiome",
199            "status": "preview",
200            "summary": "single-nucleus ATAC-seq (10x multiome)"
201        },
202        {
203            "@id": "/measurement-sets/IGVFDS0609EETP/",
204            "accession": "IGVFDS0609EETP",
205            "aliases": [
206                "igvf:corces_measurementSet_X035_G6_RNA"
207            ],
208            "file_set_type": "experimental data",
209            "lab": {
210                "title": "Ryan Corces, Gladstone Institute UCSF"
211            },
212            "preferred_assay_title": "10x multiome",
213            "status": "preview",
214            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
215        },
216        {
217            "@id": "/measurement-sets/IGVFDS7634FZRU/",
218            "accession": "IGVFDS7634FZRU",
219            "aliases": [
220                "igvf:corces_measurementSet_X035_G3_RNA"
221            ],
222            "file_set_type": "experimental data",
223            "lab": {
224                "title": "Ryan Corces, Gladstone Institute UCSF"
225            },
226            "preferred_assay_title": "10x multiome",
227            "status": "preview",
228            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
229        },
230        {
231            "@id": "/measurement-sets/IGVFDS1635NGUE/",
232            "accession": "IGVFDS1635NGUE",
233            "aliases": [
234                "igvf:corces_measurementSet_X035_G3_ATAC"
235            ],
236            "file_set_type": "experimental data",
237            "lab": {
238                "title": "Ryan Corces, Gladstone Institute UCSF"
239            },
240            "preferred_assay_title": "10x multiome",
241            "status": "preview",
242            "summary": "single-nucleus ATAC-seq (10x multiome)"
243        },
244        {
245            "@id": "/measurement-sets/IGVFDS0600TBEL/",
246            "accession": "IGVFDS0600TBEL",
247            "aliases": [
248                "igvf:corces_measurementSet_X035_G8_ATAC"
249            ],
250            "file_set_type": "experimental data",
251            "lab": {
252                "title": "Ryan Corces, Gladstone Institute UCSF"
253            },
254            "preferred_assay_title": "10x multiome",
255            "status": "preview",
256            "summary": "single-nucleus ATAC-seq (10x multiome)"
257        },
258        {
259            "@id": "/measurement-sets/IGVFDS4852MAWX/",
260            "accession": "IGVFDS4852MAWX",
261            "aliases": [
262                "igvf:corces_measurementSet_X035_G8_RNA"
263            ],
264            "file_set_type": "experimental data",
265            "lab": {
266                "title": "Ryan Corces, Gladstone Institute UCSF"
267            },
268            "preferred_assay_title": "10x multiome",
269            "status": "preview",
270            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
271        },
272        {
273            "@id": "/measurement-sets/IGVFDS0855IFDW/",
274            "accession": "IGVFDS0855IFDW",
275            "aliases": [
276                "igvf:corces_measurementSet_RP012_G2_ATAC"
277            ],
278            "file_set_type": "experimental data",
279            "lab": {
280                "title": "Ryan Corces, Gladstone Institute UCSF"
281            },
282            "preferred_assay_title": "10x multiome",
283            "status": "preview",
284            "summary": "single-nucleus ATAC-seq (10x multiome)"
285        },
286        {
287            "@id": "/measurement-sets/IGVFDS1447ZIXP/",
288            "accession": "IGVFDS1447ZIXP",
289            "aliases": [
290                "igvf:corces_measurementSet_RP012_G2_RNA"
291            ],
292            "file_set_type": "experimental data",
293            "lab": {
294                "title": "Ryan Corces, Gladstone Institute UCSF"
295            },
296            "preferred_assay_title": "10x multiome",
297            "status": "preview",
298            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
299        },
300        {
301            "@id": "/measurement-sets/IGVFDS7801ASCP/",
302            "accession": "IGVFDS7801ASCP",
303            "aliases": [
304                "igvf:corces_measurementSet_RP012_G3_ATAC"
305            ],
306            "file_set_type": "experimental data",
307            "lab": {
308                "title": "Ryan Corces, Gladstone Institute UCSF"
309            },
310            "preferred_assay_title": "10x multiome",
311            "status": "preview",
312            "summary": "single-nucleus ATAC-seq (10x multiome)"
313        },
314        {
315            "@id": "/measurement-sets/IGVFDS7235JXKZ/",
316            "accession": "IGVFDS7235JXKZ",
317            "aliases": [
318                "igvf:corces_measurementSet_RP012_G3_RNA"
319            ],
320            "file_set_type": "experimental data",
321            "lab": {
322                "title": "Ryan Corces, Gladstone Institute UCSF"
323            },
324            "preferred_assay_title": "10x multiome",
325            "status": "preview",
326            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
327        },
328        {
329            "@id": "/measurement-sets/IGVFDS3732KKVV/",
330            "accession": "IGVFDS3732KKVV",
331            "aliases": [
332                "igvf:corces_measurementSet_RP012_G6_ATAC"
333            ],
334            "file_set_type": "experimental data",
335            "lab": {
336                "title": "Ryan Corces, Gladstone Institute UCSF"
337            },
338            "preferred_assay_title": "10x multiome",
339            "status": "preview",
340            "summary": "single-nucleus ATAC-seq (10x multiome)"
341        },
342        {
343            "@id": "/measurement-sets/IGVFDS7013MCCH/",
344            "accession": "IGVFDS7013MCCH",
345            "aliases": [
346                "igvf:corces_measurementSet_RP012_G6_RNA"
347            ],
348            "file_set_type": "experimental data",
349            "lab": {
350                "title": "Ryan Corces, Gladstone Institute UCSF"
351            },
352            "preferred_assay_title": "10x multiome",
353            "status": "preview",
354            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
355        },
356        {
357            "@id": "/measurement-sets/IGVFDS1686QXQO/",
358            "accession": "IGVFDS1686QXQO",
359            "aliases": [
360                "igvf:corces_measurementSet_RP012_G8_ATAC"
361            ],
362            "file_set_type": "experimental data",
363            "lab": {
364                "title": "Ryan Corces, Gladstone Institute UCSF"
365            },
366            "preferred_assay_title": "10x multiome",
367            "status": "preview",
368            "summary": "single-nucleus ATAC-seq (10x multiome)"
369        },
370        {
371            "@id": "/measurement-sets/IGVFDS5071AEIH/",
372            "accession": "IGVFDS5071AEIH",
373            "aliases": [
374                "igvf:corces_measurementSet_RP012_G8_RNA"
375            ],
376            "file_set_type": "experimental data",
377            "lab": {
378                "title": "Ryan Corces, Gladstone Institute UCSF"
379            },
380            "preferred_assay_title": "10x multiome",
381            "status": "preview",
382            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
383        },
384        {
385            "@id": "/measurement-sets/IGVFDS7449XPIG/",
386            "accession": "IGVFDS7449XPIG",
387            "aliases": [
388                "igvf:corces_measurementSet_RP012_G4_ATAC"
389            ],
390            "file_set_type": "experimental data",
391            "lab": {
392                "title": "Ryan Corces, Gladstone Institute UCSF"
393            },
394            "preferred_assay_title": "10x multiome",
395            "status": "preview",
396            "summary": "single-nucleus ATAC-seq (10x multiome)"
397        },
398        {
399            "@id": "/measurement-sets/IGVFDS0360VRTX/",
400            "accession": "IGVFDS0360VRTX",
401            "aliases": [
402                "igvf:corces_measurementSet_RP012_G4_RNA"
403            ],
404            "file_set_type": "experimental data",
405            "lab": {
406                "title": "Ryan Corces, Gladstone Institute UCSF"
407            },
408            "preferred_assay_title": "10x multiome",
409            "status": "preview",
410            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
411        },
412        {
413            "@id": "/measurement-sets/IGVFDS5556IRJC/",
414            "accession": "IGVFDS5556IRJC",
415            "aliases": [
416                "igvf:corces_measurementSet_RP012_G7_ATAC"
417            ],
418            "file_set_type": "experimental data",
419            "lab": {
420                "title": "Ryan Corces, Gladstone Institute UCSF"
421            },
422            "preferred_assay_title": "10x multiome",
423            "status": "preview",
424            "summary": "single-nucleus ATAC-seq (10x multiome)"
425        },
426        {
427            "@id": "/measurement-sets/IGVFDS4665BFMR/",
428            "accession": "IGVFDS4665BFMR",
429            "aliases": [
430                "igvf:corces_measurementSet_RP012_G7_RNA"
431            ],
432            "file_set_type": "experimental data",
433            "lab": {
434                "title": "Ryan Corces, Gladstone Institute UCSF"
435            },
436            "preferred_assay_title": "10x multiome",
437            "status": "preview",
438            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
439        },
440        {
441            "@id": "/measurement-sets/IGVFDS8336JFEI/",
442            "accession": "IGVFDS8336JFEI",
443            "aliases": [
444                "igvf:corces_measurementSet_RP012_G1_ATAC"
445            ],
446            "file_set_type": "experimental data",
447            "lab": {
448                "title": "Ryan Corces, Gladstone Institute UCSF"
449            },
450            "preferred_assay_title": "10x multiome",
451            "status": "preview",
452            "summary": "single-nucleus ATAC-seq (10x multiome)"
453        },
454        {
455            "@id": "/measurement-sets/IGVFDS9129KQZH/",
456            "accession": "IGVFDS9129KQZH",
457            "aliases": [
458                "igvf:corces_measurementSet_RP012_G1_RNA"
459            ],
460            "file_set_type": "experimental data",
461            "lab": {
462                "title": "Ryan Corces, Gladstone Institute UCSF"
463            },
464            "preferred_assay_title": "10x multiome",
465            "status": "preview",
466            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
467        },
468        {
469            "@id": "/measurement-sets/IGVFDS2193DIJK/",
470            "accession": "IGVFDS2193DIJK",
471            "aliases": [
472                "igvf:corces_measurementSet_RP012_G5_RNA"
473            ],
474            "file_set_type": "experimental data",
475            "lab": {
476                "title": "Ryan Corces, Gladstone Institute UCSF"
477            },
478            "preferred_assay_title": "10x multiome",
479            "status": "preview",
480            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
481        },
482        {
483            "@id": "/measurement-sets/IGVFDS7068ROMA/",
484            "accession": "IGVFDS7068ROMA",
485            "aliases": [
486                "igvf:corces_measurementSet_RP012_G5_ATAC"
487            ],
488            "file_set_type": "experimental data",
489            "lab": {
490                "title": "Ryan Corces, Gladstone Institute UCSF"
491            },
492            "preferred_assay_title": "10x multiome",
493            "status": "preview",
494            "summary": "single-nucleus ATAC-seq (10x multiome)"
495        }
496    ],
497    "institutional_certificates": [
498        {
499            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
500            "certificate_identifier": "IP115-05",
501            "controlled_access": false,
502            "status": "in progress"
503        }
504    ],
505    "lab": {
506        "@id": "/labs/ryan-corces/",
507        "title": "Ryan Corces, Gladstone Institute UCSF"
508    },
509    "lower_bound_age": 89,
510    "lower_bound_age_in_hours": 779640,
511    "multiplexed_in": [
512        {
513            "@id": "/multiplexed-samples/IGVFSM2603ZBHC/",
514            "accession": "IGVFSM2603ZBHC",
515            "status": "preview"
516        },
517        {
518            "@id": "/multiplexed-samples/IGVFSM2818XKIR/",
519            "accession": "IGVFSM2818XKIR",
520            "status": "preview"
521        },
522        {
523            "@id": "/multiplexed-samples/IGVFSM7804QSQN/",
524            "accession": "IGVFSM7804QSQN",
525            "status": "preview"
526        },
527        {
528            "@id": "/multiplexed-samples/IGVFSM0834XHYE/",
529            "accession": "IGVFSM0834XHYE",
530            "status": "preview"
531        },
532        {
533            "@id": "/multiplexed-samples/IGVFSM4270KNWS/",
534            "accession": "IGVFSM4270KNWS",
535            "status": "preview"
536        },
537        {
538            "@id": "/multiplexed-samples/IGVFSM5298RMGT/",
539            "accession": "IGVFSM5298RMGT",
540            "status": "preview"
541        },
542        {
543            "@id": "/multiplexed-samples/IGVFSM7229GVNA/",
544            "accession": "IGVFSM7229GVNA",
545            "status": "preview"
546        },
547        {
548            "@id": "/multiplexed-samples/IGVFSM0431MAJD/",
549            "accession": "IGVFSM0431MAJD",
550            "status": "preview"
551        },
552        {
553            "@id": "/multiplexed-samples/IGVFSM3226MLFV/",
554            "accession": "IGVFSM3226MLFV",
555            "status": "preview"
556        },
557        {
558            "@id": "/multiplexed-samples/IGVFSM9610QWFB/",
559            "accession": "IGVFSM9610QWFB",
560            "status": "preview"
561        },
562        {
563            "@id": "/multiplexed-samples/IGVFSM5046SGAL/",
564            "accession": "IGVFSM5046SGAL",
565            "status": "preview"
566        },
567        {
568            "@id": "/multiplexed-samples/IGVFSM9167CXIN/",
569            "accession": "IGVFSM9167CXIN",
570            "status": "preview"
571        },
572        {
573            "@id": "/multiplexed-samples/IGVFSM1205XBBX/",
574            "accession": "IGVFSM1205XBBX",
575            "status": "preview"
576        },
577        {
578            "@id": "/multiplexed-samples/IGVFSM6267UURV/",
579            "accession": "IGVFSM6267UURV",
580            "status": "preview"
581        },
582        {
583            "@id": "/multiplexed-samples/IGVFSM3122KACM/",
584            "accession": "IGVFSM3122KACM",
585            "status": "preview"
586        },
587        {
588            "@id": "/multiplexed-samples/IGVFSM0752KTLR/",
589            "accession": "IGVFSM0752KTLR",
590            "status": "preview"
591        }
592    ],
593    "origin_of": [],
594    "parts": [],
595    "pmi": 150,
596    "pmi_units": "minute",
597    "pooled_in": [],
598    "preservation_method": "flash-freezing",
599    "protocols": [
600        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
601    ],
602    "sample_terms": [
603        {
604            "@id": "/sample-terms/UBERON_0002038/",
605            "status": "preview",
606            "term_name": "substantia nigra"
607        }
608    ],
609    "schema_version": "21",
610    "sex": "male",
611    "sorted_fractions": [],
612    "sources": [
613        {
614            "@id": "/sources/banner-health/",
615            "status": "released",
616            "title": "Banner Health"
617        }
618    ],
619    "status": "preview",
620    "submitted_by": {
621        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
622        "title": "Ryan Corces"
623    },
624    "summary": "Homo sapiens (male, 89 years) substantia nigra tissue",
625    "taxa": "Homo sapiens",
626    "upper_bound_age": 89,
627    "upper_bound_age_in_hours": 779640,
628    "uuid": "959fae92-671f-46d1-83ec-4c8da59dbadf",
629    "virtual": false
630}