substantia nigra — IGVFSM6107UJUH

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM6107UJUH/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM6107UJUH",
11    "age": "80",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1614_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM6107UJUH](/tissues/IGVFSM6107UJUH/) 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/IGVFSM6107UJUH/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM6107UJUH](/tissues/IGVFSM6107UJUH/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_item_status",
32                "path": "/tissues/IGVFSM6107UJUH/"
33            },
34            {
35                "category": "mismatched status",
36                "detail": "Preview tissue [IGVFSM6107UJUH](/tissues/IGVFSM6107UJUH/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
37                "level": 30,
38                "level_name": "INTERNAL_ACTION",
39                "name": "audit_item_status",
40                "path": "/tissues/IGVFSM6107UJUH/"
41            },
42            {
43                "category": "missing CCF ID",
44                "detail": "Tissue [IGVFSM6107UJUH](/tissues/IGVFSM6107UJUH/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
45                "level": 30,
46                "level_name": "INTERNAL_ACTION",
47                "name": "audit_tissue_ccf_id",
48                "path": "/tissues/IGVFSM6107UJUH/"
49            }
50        ]
51    },
52    "award": {
53        "@id": "/awards/HG012076/",
54        "component": "mapping"
55    },
56    "classifications": [
57        "tissue"
58    ],
59    "creation_timestamp": "2025-03-19T04:15:20.720500+00:00",
60    "date_obtained": "2023-03-15",
61    "disease_terms": [
62        {
63            "@id": "/phenotype-terms/DOID_14330/",
64            "status": "in progress",
65            "term_name": "Parkinson's disease"
66        },
67        {
68            "@id": "/phenotype-terms/DOID_9246/",
69            "status": "in progress",
70            "term_name": "cerebral amyloid angiopathy"
71        },
72        {
73            "@id": "/phenotype-terms/DOID_0080832/",
74            "status": "in progress",
75            "term_name": "mild cognitive impairment"
76        }
77    ],
78    "donors": [
79        {
80            "@id": "/human-donors/IGVFDO7227BIXW/",
81            "accession": "IGVFDO7227BIXW",
82            "ethnicities": [
83                "European"
84            ],
85            "status": "preview"
86        }
87    ],
88    "file_sets": [
89        {
90            "@id": "/measurement-sets/IGVFDS9165PGZO/",
91            "accession": "IGVFDS9165PGZO",
92            "aliases": [
93                "igvf:corces_measurementSet_X045_G2_ATAC"
94            ],
95            "file_set_type": "experimental data",
96            "lab": {
97                "title": "Ryan Corces, Gladstone Institute UCSF"
98            },
99            "preferred_assay_title": "10x multiome",
100            "status": "preview",
101            "summary": "single-nucleus ATAC-seq (10x multiome)"
102        },
103        {
104            "@id": "/measurement-sets/IGVFDS2373KVYV/",
105            "accession": "IGVFDS2373KVYV",
106            "aliases": [
107                "igvf:corces_measurementSet_X045_G2_RNA"
108            ],
109            "file_set_type": "experimental data",
110            "lab": {
111                "title": "Ryan Corces, Gladstone Institute UCSF"
112            },
113            "preferred_assay_title": "10x multiome",
114            "status": "preview",
115            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
116        },
117        {
118            "@id": "/measurement-sets/IGVFDS2905ZOTV/",
119            "accession": "IGVFDS2905ZOTV",
120            "aliases": [
121                "igvf:corces_measurementSet_RP008_G6_ATAC"
122            ],
123            "file_set_type": "experimental data",
124            "lab": {
125                "title": "Ryan Corces, Gladstone Institute UCSF"
126            },
127            "preferred_assay_title": "10x multiome",
128            "status": "preview",
129            "summary": "single-nucleus ATAC-seq (10x multiome)"
130        },
131        {
132            "@id": "/measurement-sets/IGVFDS1310UDQP/",
133            "accession": "IGVFDS1310UDQP",
134            "aliases": [
135                "igvf:corces_measurementSet_RP008_G6_RNA"
136            ],
137            "file_set_type": "experimental data",
138            "lab": {
139                "title": "Ryan Corces, Gladstone Institute UCSF"
140            },
141            "preferred_assay_title": "10x multiome",
142            "status": "preview",
143            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
144        },
145        {
146            "@id": "/measurement-sets/IGVFDS6197EMPG/",
147            "accession": "IGVFDS6197EMPG",
148            "aliases": [
149                "igvf:corces_measurementSet_RP008_G1_ATAC"
150            ],
151            "file_set_type": "experimental data",
152            "lab": {
153                "title": "Ryan Corces, Gladstone Institute UCSF"
154            },
155            "preferred_assay_title": "10x multiome",
156            "status": "preview",
157            "summary": "single-nucleus ATAC-seq (10x multiome)"
158        },
159        {
160            "@id": "/measurement-sets/IGVFDS8376IRHS/",
161            "accession": "IGVFDS8376IRHS",
162            "aliases": [
163                "igvf:corces_measurementSet_RP008_G1_RNA"
164            ],
165            "file_set_type": "experimental data",
166            "lab": {
167                "title": "Ryan Corces, Gladstone Institute UCSF"
168            },
169            "preferred_assay_title": "10x multiome",
170            "status": "preview",
171            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
172        },
173        {
174            "@id": "/measurement-sets/IGVFDS7412ZECB/",
175            "accession": "IGVFDS7412ZECB",
176            "aliases": [
177                "igvf:corces_measurementSet_X045_G5_ATAC"
178            ],
179            "file_set_type": "experimental data",
180            "lab": {
181                "title": "Ryan Corces, Gladstone Institute UCSF"
182            },
183            "preferred_assay_title": "10x multiome",
184            "status": "preview",
185            "summary": "single-nucleus ATAC-seq (10x multiome)"
186        },
187        {
188            "@id": "/measurement-sets/IGVFDS9480SSTX/",
189            "accession": "IGVFDS9480SSTX",
190            "aliases": [
191                "igvf:corces_measurementSet_X045_G5_RNA"
192            ],
193            "file_set_type": "experimental data",
194            "lab": {
195                "title": "Ryan Corces, Gladstone Institute UCSF"
196            },
197            "preferred_assay_title": "10x multiome",
198            "status": "preview",
199            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
200        },
201        {
202            "@id": "/measurement-sets/IGVFDS9847KZJV/",
203            "accession": "IGVFDS9847KZJV",
204            "aliases": [
205                "igvf:corces_measurementSet_X045_G7_ATAC"
206            ],
207            "file_set_type": "experimental data",
208            "lab": {
209                "title": "Ryan Corces, Gladstone Institute UCSF"
210            },
211            "preferred_assay_title": "10x multiome",
212            "status": "preview",
213            "summary": "single-nucleus ATAC-seq (10x multiome)"
214        },
215        {
216            "@id": "/measurement-sets/IGVFDS0170SDNB/",
217            "accession": "IGVFDS0170SDNB",
218            "aliases": [
219                "igvf:corces_measurementSet_X045_G7_RNA"
220            ],
221            "file_set_type": "experimental data",
222            "lab": {
223                "title": "Ryan Corces, Gladstone Institute UCSF"
224            },
225            "preferred_assay_title": "10x multiome",
226            "status": "preview",
227            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
228        },
229        {
230            "@id": "/measurement-sets/IGVFDS2244JUGR/",
231            "accession": "IGVFDS2244JUGR",
232            "aliases": [
233                "igvf:corces_measurementSet_X045_G1_ATAC"
234            ],
235            "file_set_type": "experimental data",
236            "lab": {
237                "title": "Ryan Corces, Gladstone Institute UCSF"
238            },
239            "preferred_assay_title": "10x multiome",
240            "status": "preview",
241            "summary": "single-nucleus ATAC-seq (10x multiome)"
242        },
243        {
244            "@id": "/measurement-sets/IGVFDS3164XQLE/",
245            "accession": "IGVFDS3164XQLE",
246            "aliases": [
247                "igvf:corces_measurementSet_X045_G1_RNA"
248            ],
249            "file_set_type": "experimental data",
250            "lab": {
251                "title": "Ryan Corces, Gladstone Institute UCSF"
252            },
253            "preferred_assay_title": "10x multiome",
254            "status": "preview",
255            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
256        },
257        {
258            "@id": "/measurement-sets/IGVFDS6181AGCI/",
259            "accession": "IGVFDS6181AGCI",
260            "aliases": [
261                "igvf:corces_measurementSet_X045_G3_ATAC"
262            ],
263            "file_set_type": "experimental data",
264            "lab": {
265                "title": "Ryan Corces, Gladstone Institute UCSF"
266            },
267            "preferred_assay_title": "10x multiome",
268            "status": "preview",
269            "summary": "single-nucleus ATAC-seq (10x multiome)"
270        },
271        {
272            "@id": "/measurement-sets/IGVFDS3516DUWU/",
273            "accession": "IGVFDS3516DUWU",
274            "aliases": [
275                "igvf:corces_measurementSet_X045_G3_RNA"
276            ],
277            "file_set_type": "experimental data",
278            "lab": {
279                "title": "Ryan Corces, Gladstone Institute UCSF"
280            },
281            "preferred_assay_title": "10x multiome",
282            "status": "preview",
283            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
284        },
285        {
286            "@id": "/measurement-sets/IGVFDS4033UDFN/",
287            "accession": "IGVFDS4033UDFN",
288            "aliases": [
289                "igvf:corces_measurementSet_X045_G8_ATAC"
290            ],
291            "file_set_type": "experimental data",
292            "lab": {
293                "title": "Ryan Corces, Gladstone Institute UCSF"
294            },
295            "preferred_assay_title": "10x multiome",
296            "status": "preview",
297            "summary": "single-nucleus ATAC-seq (10x multiome)"
298        },
299        {
300            "@id": "/measurement-sets/IGVFDS2415CEXM/",
301            "accession": "IGVFDS2415CEXM",
302            "aliases": [
303                "igvf:corces_measurementSet_X045_G8_RNA"
304            ],
305            "file_set_type": "experimental data",
306            "lab": {
307                "title": "Ryan Corces, Gladstone Institute UCSF"
308            },
309            "preferred_assay_title": "10x multiome",
310            "status": "preview",
311            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
312        },
313        {
314            "@id": "/measurement-sets/IGVFDS1106JKWP/",
315            "accession": "IGVFDS1106JKWP",
316            "aliases": [
317                "igvf:corces_measurementSet_X045_G4_ATAC"
318            ],
319            "file_set_type": "experimental data",
320            "lab": {
321                "title": "Ryan Corces, Gladstone Institute UCSF"
322            },
323            "preferred_assay_title": "10x multiome",
324            "status": "preview",
325            "summary": "single-nucleus ATAC-seq (10x multiome)"
326        },
327        {
328            "@id": "/measurement-sets/IGVFDS7523ZOWN/",
329            "accession": "IGVFDS7523ZOWN",
330            "aliases": [
331                "igvf:corces_measurementSet_X045_G4_RNA"
332            ],
333            "file_set_type": "experimental data",
334            "lab": {
335                "title": "Ryan Corces, Gladstone Institute UCSF"
336            },
337            "preferred_assay_title": "10x multiome",
338            "status": "preview",
339            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
340        },
341        {
342            "@id": "/measurement-sets/IGVFDS2994XKQR/",
343            "accession": "IGVFDS2994XKQR",
344            "aliases": [
345                "igvf:corces_measurementSet_X045_G6_ATAC"
346            ],
347            "file_set_type": "experimental data",
348            "lab": {
349                "title": "Ryan Corces, Gladstone Institute UCSF"
350            },
351            "preferred_assay_title": "10x multiome",
352            "status": "preview",
353            "summary": "single-nucleus ATAC-seq (10x multiome)"
354        },
355        {
356            "@id": "/measurement-sets/IGVFDS8668VCFD/",
357            "accession": "IGVFDS8668VCFD",
358            "aliases": [
359                "igvf:corces_measurementSet_X045_G6_RNA"
360            ],
361            "file_set_type": "experimental data",
362            "lab": {
363                "title": "Ryan Corces, Gladstone Institute UCSF"
364            },
365            "preferred_assay_title": "10x multiome",
366            "status": "preview",
367            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
368        },
369        {
370            "@id": "/measurement-sets/IGVFDS6713WNIZ/",
371            "accession": "IGVFDS6713WNIZ",
372            "aliases": [
373                "igvf:corces_measurementSet_RP008_G3_ATAC"
374            ],
375            "file_set_type": "experimental data",
376            "lab": {
377                "title": "Ryan Corces, Gladstone Institute UCSF"
378            },
379            "preferred_assay_title": "10x multiome",
380            "status": "preview",
381            "summary": "single-nucleus ATAC-seq (10x multiome)"
382        },
383        {
384            "@id": "/measurement-sets/IGVFDS9648TFEB/",
385            "accession": "IGVFDS9648TFEB",
386            "aliases": [
387                "igvf:corces_measurementSet_RP008_G3_RNA"
388            ],
389            "file_set_type": "experimental data",
390            "lab": {
391                "title": "Ryan Corces, Gladstone Institute UCSF"
392            },
393            "preferred_assay_title": "10x multiome",
394            "status": "preview",
395            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
396        },
397        {
398            "@id": "/measurement-sets/IGVFDS9259SQOO/",
399            "accession": "IGVFDS9259SQOO",
400            "aliases": [
401                "igvf:corces_measurementSet_RP008_G2_ATAC"
402            ],
403            "file_set_type": "experimental data",
404            "lab": {
405                "title": "Ryan Corces, Gladstone Institute UCSF"
406            },
407            "preferred_assay_title": "10x multiome",
408            "status": "preview",
409            "summary": "single-nucleus ATAC-seq (10x multiome)"
410        },
411        {
412            "@id": "/measurement-sets/IGVFDS1106CBKV/",
413            "accession": "IGVFDS1106CBKV",
414            "aliases": [
415                "igvf:corces_measurementSet_RP008_G2_RNA"
416            ],
417            "file_set_type": "experimental data",
418            "lab": {
419                "title": "Ryan Corces, Gladstone Institute UCSF"
420            },
421            "preferred_assay_title": "10x multiome",
422            "status": "preview",
423            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
424        },
425        {
426            "@id": "/measurement-sets/IGVFDS8701BRPU/",
427            "accession": "IGVFDS8701BRPU",
428            "aliases": [
429                "igvf:corces_measurementSet_RP008_G8_ATAC"
430            ],
431            "file_set_type": "experimental data",
432            "lab": {
433                "title": "Ryan Corces, Gladstone Institute UCSF"
434            },
435            "preferred_assay_title": "10x multiome",
436            "status": "preview",
437            "summary": "single-nucleus ATAC-seq (10x multiome)"
438        },
439        {
440            "@id": "/measurement-sets/IGVFDS6991WMGS/",
441            "accession": "IGVFDS6991WMGS",
442            "aliases": [
443                "igvf:corces_measurementSet_RP008_G8_RNA"
444            ],
445            "file_set_type": "experimental data",
446            "lab": {
447                "title": "Ryan Corces, Gladstone Institute UCSF"
448            },
449            "preferred_assay_title": "10x multiome",
450            "status": "preview",
451            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
452        },
453        {
454            "@id": "/measurement-sets/IGVFDS1740NBJU/",
455            "accession": "IGVFDS1740NBJU",
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457                "igvf:corces_measurementSet_RP008_G7_ATAC"
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460            "lab": {
461                "title": "Ryan Corces, Gladstone Institute UCSF"
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463            "preferred_assay_title": "10x multiome",
464            "status": "preview",
465            "summary": "single-nucleus ATAC-seq (10x multiome)"
466        },
467        {
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470            "aliases": [
471                "igvf:corces_measurementSet_RP008_G7_RNA"
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474            "lab": {
475                "title": "Ryan Corces, Gladstone Institute UCSF"
476            },
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478            "status": "preview",
479            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
480        },
481        {
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488            "lab": {
489                "title": "Ryan Corces, Gladstone Institute UCSF"
490            },
491            "preferred_assay_title": "10x multiome",
492            "status": "preview",
493            "summary": "single-nucleus ATAC-seq (10x multiome)"
494        },
495        {
496            "@id": "/measurement-sets/IGVFDS6803UPKV/",
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498            "aliases": [
499                "igvf:corces_measurementSet_RP008_G5_RNA"
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501            "file_set_type": "experimental data",
502            "lab": {
503                "title": "Ryan Corces, Gladstone Institute UCSF"
504            },
505            "preferred_assay_title": "10x multiome",
506            "status": "preview",
507            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
508        },
509        {
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511            "accession": "IGVFDS8288FNQQ",
512            "aliases": [
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515            "file_set_type": "experimental data",
516            "lab": {
517                "title": "Ryan Corces, Gladstone Institute UCSF"
518            },
519            "preferred_assay_title": "10x multiome",
520            "status": "preview",
521            "summary": "single-nucleus ATAC-seq (10x multiome)"
522        },
523        {
524            "@id": "/measurement-sets/IGVFDS7062QEKO/",
525            "accession": "IGVFDS7062QEKO",
526            "aliases": [
527                "igvf:corces_measurementSet_RP008_G4_RNA"
528            ],
529            "file_set_type": "experimental data",
530            "lab": {
531                "title": "Ryan Corces, Gladstone Institute UCSF"
532            },
533            "preferred_assay_title": "10x multiome",
534            "status": "preview",
535            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
536        }
537    ],
538    "institutional_certificates": [
539        {
540            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
541            "certificate_identifier": "IP115-05",
542            "controlled_access": false,
543            "status": "in progress"
544        }
545    ],
546    "lab": {
547        "@id": "/labs/ryan-corces/",
548        "title": "Ryan Corces, Gladstone Institute UCSF"
549    },
550    "lower_bound_age": 80,
551    "lower_bound_age_in_hours": 700800,
552    "multiplexed_in": [
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562        },
563        {
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565            "accession": "IGVFSM3315GFKX",
566            "status": "preview"
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568        {
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571            "status": "preview"
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573        {
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575            "accession": "IGVFSM3071DTOY",
576            "status": "preview"
577        },
578        {
579            "@id": "/multiplexed-samples/IGVFSM2472IWEH/",
580            "accession": "IGVFSM2472IWEH",
581            "status": "preview"
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583        {
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585            "accession": "IGVFSM7137FCCD",
586            "status": "preview"
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588        {
589            "@id": "/multiplexed-samples/IGVFSM3519VNVW/",
590            "accession": "IGVFSM3519VNVW",
591            "status": "preview"
592        },
593        {
594            "@id": "/multiplexed-samples/IGVFSM8872IRZA/",
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596            "status": "preview"
597        },
598        {
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606            "status": "preview"
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610            "accession": "IGVFSM5834KBZJ",
611            "status": "preview"
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613        {
614            "@id": "/multiplexed-samples/IGVFSM9455XPMQ/",
615            "accession": "IGVFSM9455XPMQ",
616            "status": "preview"
617        },
618        {
619            "@id": "/multiplexed-samples/IGVFSM8027AHHD/",
620            "accession": "IGVFSM8027AHHD",
621            "status": "preview"
622        },
623        {
624            "@id": "/multiplexed-samples/IGVFSM1888IYGT/",
625            "accession": "IGVFSM1888IYGT",
626            "status": "preview"
627        },
628        {
629            "@id": "/multiplexed-samples/IGVFSM1461ETOM/",
630            "accession": "IGVFSM1461ETOM",
631            "status": "preview"
632        }
633    ],
634    "origin_of": [],
635    "parts": [],
636    "pmi": 156,
637    "pmi_units": "minute",
638    "pooled_in": [],
639    "preservation_method": "flash-freezing",
640    "protocols": [
641        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
642    ],
643    "sample_terms": [
644        {
645            "@id": "/sample-terms/UBERON_0002038/",
646            "status": "preview",
647            "term_name": "substantia nigra"
648        }
649    ],
650    "schema_version": "21",
651    "sex": "male",
652    "sorted_fractions": [],
653    "sources": [
654        {
655            "@id": "/sources/banner-health/",
656            "status": "released",
657            "title": "Banner Health"
658        }
659    ],
660    "status": "preview",
661    "submitted_by": {
662        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
663        "title": "Ryan Corces"
664    },
665    "summary": "Homo sapiens (male, 80 years) substantia nigra tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
666    "taxa": "Homo sapiens",
667    "upper_bound_age": 80,
668    "upper_bound_age_in_hours": 700800,
669    "uuid": "b88aee5e-d9f8-40e1-ad0a-83b9f9fb1e9c",
670    "virtual": false
671}