substantia nigra — IGVFSM2235SCZO

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM2235SCZO/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM2235SCZO",
11    "age": "84",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1959_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM2235SCZO](/tissues/IGVFSM2235SCZO/) 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/IGVFSM2235SCZO/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM2235SCZO](/tissues/IGVFSM2235SCZO/) 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/IGVFSM2235SCZO/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T04:15:45.603798+00:00",
44    "date_obtained": "2023-03-16",
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/IGVFDO3501RYHX/",
55            "accession": "IGVFDO3501RYHX",
56            "ethnicities": [
57                "European"
58            ],
59            "status": "preview"
60        }
61    ],
62    "file_sets": [
63        {
64            "@id": "/measurement-sets/IGVFDS1028ZFVQ/",
65            "accession": "IGVFDS1028ZFVQ",
66            "aliases": [
67                "igvf:corces_measurementSet_X047_G8_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/IGVFDS1618GVTK/",
79            "accession": "IGVFDS1618GVTK",
80            "aliases": [
81                "igvf:corces_measurementSet_X047_G8_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/IGVFDS1986QXQD/",
93            "accession": "IGVFDS1986QXQD",
94            "aliases": [
95                "igvf:corces_measurementSet_X047_G1_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/IGVFDS5124VXCN/",
107            "accession": "IGVFDS5124VXCN",
108            "aliases": [
109                "igvf:corces_measurementSet_X047_G1_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/IGVFDS4670XLUZ/",
121            "accession": "IGVFDS4670XLUZ",
122            "aliases": [
123                "igvf:corces_measurementSet_X047_G6_ATAC"
124            ],
125            "file_set_type": "experimental data",
126            "lab": {
127                "title": "Ryan Corces, Gladstone Institute UCSF"
128            },
129            "preferred_assay_title": "10x multiome",
130            "status": "preview",
131            "summary": "single-nucleus ATAC-seq (10x multiome)"
132        },
133        {
134            "@id": "/measurement-sets/IGVFDS9092LXII/",
135            "accession": "IGVFDS9092LXII",
136            "aliases": [
137                "igvf:corces_measurementSet_X047_G6_RNA"
138            ],
139            "file_set_type": "experimental data",
140            "lab": {
141                "title": "Ryan Corces, Gladstone Institute UCSF"
142            },
143            "preferred_assay_title": "10x multiome",
144            "status": "preview",
145            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
146        },
147        {
148            "@id": "/measurement-sets/IGVFDS8347THAT/",
149            "accession": "IGVFDS8347THAT",
150            "aliases": [
151                "igvf:corces_measurementSet_X047_G4_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/IGVFDS0432HLKO/",
163            "accession": "IGVFDS0432HLKO",
164            "aliases": [
165                "igvf:corces_measurementSet_X047_G4_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/IGVFDS5084VXAN/",
177            "accession": "IGVFDS5084VXAN",
178            "aliases": [
179                "igvf:corces_measurementSet_X047_G5_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/IGVFDS6107XJBQ/",
191            "accession": "IGVFDS6107XJBQ",
192            "aliases": [
193                "igvf:corces_measurementSet_X047_G5_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/IGVFDS5940RHAE/",
205            "accession": "IGVFDS5940RHAE",
206            "aliases": [
207                "igvf:corces_measurementSet_X047_G2_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/IGVFDS0224PFFL/",
219            "accession": "IGVFDS0224PFFL",
220            "aliases": [
221                "igvf:corces_measurementSet_X047_G2_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/IGVFDS5283BQYM/",
233            "accession": "IGVFDS5283BQYM",
234            "aliases": [
235                "igvf:corces_measurementSet_X047_G3_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/IGVFDS8758TSKY/",
247            "accession": "IGVFDS8758TSKY",
248            "aliases": [
249                "igvf:corces_measurementSet_X047_G3_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/IGVFDS5875ONDA/",
261            "accession": "IGVFDS5875ONDA",
262            "aliases": [
263                "igvf:corces_measurementSet_X047_G7_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/IGVFDS7159LGSK/",
275            "accession": "IGVFDS7159LGSK",
276            "aliases": [
277                "igvf:corces_measurementSet_X047_G7_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/IGVFDS5362QJCF/",
289            "accession": "IGVFDS5362QJCF",
290            "aliases": [
291                "igvf:corces_measurementSet_RP011_G3_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/IGVFDS1279DJVE/",
303            "accession": "IGVFDS1279DJVE",
304            "aliases": [
305                "igvf:corces_measurementSet_RP011_G3_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/IGVFDS8666KHZN/",
317            "accession": "IGVFDS8666KHZN",
318            "aliases": [
319                "igvf:corces_measurementSet_RP011_G2_ATAC"
320            ],
321            "file_set_type": "experimental data",
322            "lab": {
323                "title": "Ryan Corces, Gladstone Institute UCSF"
324            },
325            "preferred_assay_title": "10x multiome",
326            "status": "preview",
327            "summary": "single-nucleus ATAC-seq (10x multiome)"
328        },
329        {
330            "@id": "/measurement-sets/IGVFDS7806UOQI/",
331            "accession": "IGVFDS7806UOQI",
332            "aliases": [
333                "igvf:corces_measurementSet_RP011_G2_RNA"
334            ],
335            "file_set_type": "experimental data",
336            "lab": {
337                "title": "Ryan Corces, Gladstone Institute UCSF"
338            },
339            "preferred_assay_title": "10x multiome",
340            "status": "preview",
341            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
342        },
343        {
344            "@id": "/measurement-sets/IGVFDS0856IUPF/",
345            "accession": "IGVFDS0856IUPF",
346            "aliases": [
347                "igvf:corces_measurementSet_RP011_G6_ATAC"
348            ],
349            "file_set_type": "experimental data",
350            "lab": {
351                "title": "Ryan Corces, Gladstone Institute UCSF"
352            },
353            "preferred_assay_title": "10x multiome",
354            "status": "preview",
355            "summary": "single-nucleus ATAC-seq (10x multiome)"
356        },
357        {
358            "@id": "/measurement-sets/IGVFDS8611TPMB/",
359            "accession": "IGVFDS8611TPMB",
360            "aliases": [
361                "igvf:corces_measurementSet_RP011_G6_RNA"
362            ],
363            "file_set_type": "experimental data",
364            "lab": {
365                "title": "Ryan Corces, Gladstone Institute UCSF"
366            },
367            "preferred_assay_title": "10x multiome",
368            "status": "preview",
369            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
370        },
371        {
372            "@id": "/measurement-sets/IGVFDS3484DNVB/",
373            "accession": "IGVFDS3484DNVB",
374            "aliases": [
375                "igvf:corces_measurementSet_RP011_G5_RNA"
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 RNA sequencing assay (10x multiome)"
384        },
385        {
386            "@id": "/measurement-sets/IGVFDS3602NEYS/",
387            "accession": "IGVFDS3602NEYS",
388            "aliases": [
389                "igvf:corces_measurementSet_RP011_G5_ATAC"
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 ATAC-seq (10x multiome)"
398        },
399        {
400            "@id": "/measurement-sets/IGVFDS5146PTIC/",
401            "accession": "IGVFDS5146PTIC",
402            "aliases": [
403                "igvf:corces_measurementSet_RP011_G7_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/IGVFDS2300TLPU/",
415            "accession": "IGVFDS2300TLPU",
416            "aliases": [
417                "igvf:corces_measurementSet_RP011_G7_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/IGVFDS2229EHIM/",
429            "accession": "IGVFDS2229EHIM",
430            "aliases": [
431                "igvf:corces_measurementSet_RP011_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/IGVFDS3628MXUK/",
443            "accession": "IGVFDS3628MXUK",
444            "aliases": [
445                "igvf:corces_measurementSet_RP011_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/IGVFDS0831CAYJ/",
457            "accession": "IGVFDS0831CAYJ",
458            "aliases": [
459                "igvf:corces_measurementSet_RP011_G4_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/IGVFDS4334WKOE/",
471            "accession": "IGVFDS4334WKOE",
472            "aliases": [
473                "igvf:corces_measurementSet_RP011_G4_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            "@id": "/measurement-sets/IGVFDS3035QFKU/",
485            "accession": "IGVFDS3035QFKU",
486            "aliases": [
487                "igvf:corces_measurementSet_RP011_G8_ATAC"
488            ],
489            "file_set_type": "experimental data",
490            "lab": {
491                "title": "Ryan Corces, Gladstone Institute UCSF"
492            },
493            "preferred_assay_title": "10x multiome",
494            "status": "preview",
495            "summary": "single-nucleus ATAC-seq (10x multiome)"
496        },
497        {
498            "@id": "/measurement-sets/IGVFDS6373YBDI/",
499            "accession": "IGVFDS6373YBDI",
500            "aliases": [
501                "igvf:corces_measurementSet_RP011_G8_RNA"
502            ],
503            "file_set_type": "experimental data",
504            "lab": {
505                "title": "Ryan Corces, Gladstone Institute UCSF"
506            },
507            "preferred_assay_title": "10x multiome",
508            "status": "preview",
509            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
510        }
511    ],
512    "institutional_certificates": [
513        {
514            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
515            "certificate_identifier": "IP115-05",
516            "controlled_access": false,
517            "status": "in progress"
518        }
519    ],
520    "lab": {
521        "@id": "/labs/ryan-corces/",
522        "title": "Ryan Corces, Gladstone Institute UCSF"
523    },
524    "lower_bound_age": 84,
525    "lower_bound_age_in_hours": 735840,
526    "multiplexed_in": [
527        {
528            "@id": "/multiplexed-samples/IGVFSM1698LTIY/",
529            "accession": "IGVFSM1698LTIY",
530            "status": "preview"
531        },
532        {
533            "@id": "/multiplexed-samples/IGVFSM6392OCPY/",
534            "accession": "IGVFSM6392OCPY",
535            "status": "preview"
536        },
537        {
538            "@id": "/multiplexed-samples/IGVFSM5457GRUY/",
539            "accession": "IGVFSM5457GRUY",
540            "status": "preview"
541        },
542        {
543            "@id": "/multiplexed-samples/IGVFSM5102POBA/",
544            "accession": "IGVFSM5102POBA",
545            "status": "preview"
546        },
547        {
548            "@id": "/multiplexed-samples/IGVFSM1695CPQZ/",
549            "accession": "IGVFSM1695CPQZ",
550            "status": "preview"
551        },
552        {
553            "@id": "/multiplexed-samples/IGVFSM8877ZHHC/",
554            "accession": "IGVFSM8877ZHHC",
555            "status": "preview"
556        },
557        {
558            "@id": "/multiplexed-samples/IGVFSM0045HDEA/",
559            "accession": "IGVFSM0045HDEA",
560            "status": "preview"
561        },
562        {
563            "@id": "/multiplexed-samples/IGVFSM7544TQQI/",
564            "accession": "IGVFSM7544TQQI",
565            "status": "preview"
566        },
567        {
568            "@id": "/multiplexed-samples/IGVFSM0695RJYV/",
569            "accession": "IGVFSM0695RJYV",
570            "status": "preview"
571        },
572        {
573            "@id": "/multiplexed-samples/IGVFSM9347ZBKI/",
574            "accession": "IGVFSM9347ZBKI",
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/IGVFSM3747QRCH/",
604            "accession": "IGVFSM3747QRCH",
605            "status": "preview"
606        }
607    ],
608    "origin_of": [],
609    "parts": [],
610    "pmi": 244,
611    "pmi_units": "minute",
612    "pooled_in": [],
613    "preservation_method": "flash-freezing",
614    "protocols": [
615        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
616    ],
617    "sample_terms": [
618        {
619            "@id": "/sample-terms/UBERON_0002038/",
620            "status": "preview",
621            "term_name": "substantia nigra"
622        }
623    ],
624    "schema_version": "21",
625    "sex": "male",
626    "sorted_fractions": [],
627    "sources": [
628        {
629            "@id": "/sources/banner-health/",
630            "status": "released",
631            "title": "Banner Health"
632        }
633    ],
634    "status": "preview",
635    "submitted_by": {
636        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
637        "title": "Ryan Corces"
638    },
639    "summary": "Homo sapiens (male, 84 years) substantia nigra tissue associated with Parkinson's disease",
640    "taxa": "Homo sapiens",
641    "upper_bound_age": 84,
642    "upper_bound_age_in_hours": 735840,
643    "uuid": "18f429f1-6223-4486-9646-1faf44a9a2dc",
644    "virtual": false
645}