substantia nigra — IGVFSM8416QDUR

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM8416QDUR/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM8416QDUR",
11    "age": "78",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1623_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM8416QDUR](/tissues/IGVFSM8416QDUR/) 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/IGVFSM8416QDUR/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM8416QDUR](/tissues/IGVFSM8416QDUR/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_item_status",
32                "path": "/tissues/IGVFSM8416QDUR/"
33            },
34            {
35                "category": "missing CCF ID",
36                "detail": "Tissue [IGVFSM8416QDUR](/tissues/IGVFSM8416QDUR/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
37                "level": 30,
38                "level_name": "INTERNAL_ACTION",
39                "name": "audit_tissue_ccf_id",
40                "path": "/tissues/IGVFSM8416QDUR/"
41            }
42        ]
43    },
44    "award": {
45        "@id": "/awards/HG012076/",
46        "component": "mapping"
47    },
48    "classifications": [
49        "tissue"
50    ],
51    "creation_timestamp": "2025-03-19T04:14:31.148556+00:00",
52    "date_obtained": "2023-03-07",
53    "disease_terms": [
54        {
55            "@id": "/phenotype-terms/DOID_14330/",
56            "status": "in progress",
57            "term_name": "Parkinson's disease"
58        },
59        {
60            "@id": "/phenotype-terms/DOID_0080832/",
61            "status": "in progress",
62            "term_name": "mild cognitive impairment"
63        }
64    ],
65    "donors": [
66        {
67            "@id": "/human-donors/IGVFDO8458OKEW/",
68            "accession": "IGVFDO8458OKEW",
69            "ethnicities": [
70                "European"
71            ],
72            "status": "preview"
73        }
74    ],
75    "file_sets": [
76        {
77            "@id": "/measurement-sets/IGVFDS3083RFCQ/",
78            "accession": "IGVFDS3083RFCQ",
79            "aliases": [
80                "igvf:corces_measurementSet_X041_G1_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/IGVFDS1691KPWU/",
92            "accession": "IGVFDS1691KPWU",
93            "aliases": [
94                "igvf:corces_measurementSet_X041_G1_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/IGVFDS9809VXKU/",
106            "accession": "IGVFDS9809VXKU",
107            "aliases": [
108                "igvf:corces_measurementSet_X041_G3_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/IGVFDS6769MHJX/",
120            "accession": "IGVFDS6769MHJX",
121            "aliases": [
122                "igvf:corces_measurementSet_X041_G3_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/IGVFDS5236WFMM/",
134            "accession": "IGVFDS5236WFMM",
135            "aliases": [
136                "igvf:corces_measurementSet_X041_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/IGVFDS8913NULI/",
148            "accession": "IGVFDS8913NULI",
149            "aliases": [
150                "igvf:corces_measurementSet_X041_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/IGVFDS7843JHRO/",
162            "accession": "IGVFDS7843JHRO",
163            "aliases": [
164                "igvf:corces_measurementSet_X041_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/IGVFDS7314VGYF/",
176            "accession": "IGVFDS7314VGYF",
177            "aliases": [
178                "igvf:corces_measurementSet_X041_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        {
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190            "accession": "IGVFDS4454OQTQ",
191            "aliases": [
192                "igvf:corces_measurementSet_X041_G7_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/IGVFDS3636ZYTF/",
204            "accession": "IGVFDS3636ZYTF",
205            "aliases": [
206                "igvf:corces_measurementSet_X041_G7_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/IGVFDS5800WXVK/",
218            "accession": "IGVFDS5800WXVK",
219            "aliases": [
220                "igvf:corces_measurementSet_X041_G5_ATAC"
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 ATAC-seq (10x multiome)"
229        },
230        {
231            "@id": "/measurement-sets/IGVFDS2612AYOV/",
232            "accession": "IGVFDS2612AYOV",
233            "aliases": [
234                "igvf:corces_measurementSet_X041_G5_RNA"
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 RNA sequencing assay (10x multiome)"
243        },
244        {
245            "@id": "/measurement-sets/IGVFDS6077CQVA/",
246            "accession": "IGVFDS6077CQVA",
247            "aliases": [
248                "igvf:corces_measurementSet_X041_G6_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/IGVFDS5006HOVG/",
260            "accession": "IGVFDS5006HOVG",
261            "aliases": [
262                "igvf:corces_measurementSet_X041_G6_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        },
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274            "accession": "IGVFDS0738WMFX",
275            "aliases": [
276                "igvf:corces_measurementSet_X041_G8_RNA"
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 RNA sequencing assay (10x multiome)"
285        },
286        {
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290                "igvf:corces_measurementSet_X041_G8_ATAC"
291            ],
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293            "lab": {
294                "title": "Ryan Corces, Gladstone Institute UCSF"
295            },
296            "preferred_assay_title": "10x multiome",
297            "status": "preview",
298            "summary": "single-nucleus ATAC-seq (10x multiome)"
299        },
300        {
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302            "accession": "IGVFDS2943LQHU",
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304                "igvf:corces_measurementSet_RP014_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/IGVFDS3707VRFM/",
316            "accession": "IGVFDS3707VRFM",
317            "aliases": [
318                "igvf:corces_measurementSet_RP014_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        {
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330            "accession": "IGVFDS7788KKVV",
331            "aliases": [
332                "igvf:corces_measurementSet_RP014_G2_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/IGVFDS3071BBZO/",
344            "accession": "IGVFDS3071BBZO",
345            "aliases": [
346                "igvf:corces_measurementSet_RP014_G2_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/IGVFDS3473OBBZ/",
358            "accession": "IGVFDS3473OBBZ",
359            "aliases": [
360                "igvf:corces_measurementSet_RP014_G8_RNA"
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 RNA sequencing assay (10x multiome)"
369        },
370        {
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372            "accession": "IGVFDS5184YEZB",
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374                "igvf:corces_measurementSet_RP014_G8_ATAC"
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 ATAC-seq (10x multiome)"
383        },
384        {
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388                "igvf:corces_measurementSet_RP014_G4_ATAC"
389            ],
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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        {
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401            "aliases": [
402                "igvf:corces_measurementSet_RP014_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        {
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416                "igvf:corces_measurementSet_RP014_G5_ATAC"
417            ],
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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        {
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429            "aliases": [
430                "igvf:corces_measurementSet_RP014_G5_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        {
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447            "lab": {
448                "title": "Ryan Corces, Gladstone Institute UCSF"
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451            "status": "preview",
452            "summary": "single-nucleus ATAC-seq (10x multiome)"
453        },
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462                "title": "Ryan Corces, Gladstone Institute UCSF"
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466            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
467        },
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475            "lab": {
476                "title": "Ryan Corces, Gladstone Institute UCSF"
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479            "status": "preview",
480            "summary": "single-nucleus ATAC-seq (10x multiome)"
481        },
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489            "lab": {
490                "title": "Ryan Corces, Gladstone Institute UCSF"
491            },
492            "preferred_assay_title": "10x multiome",
493            "status": "preview",
494            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
495        },
496        {
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503            "lab": {
504                "title": "Ryan Corces, Gladstone Institute UCSF"
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506            "preferred_assay_title": "10x multiome",
507            "status": "preview",
508            "summary": "single-nucleus ATAC-seq (10x multiome)"
509        },
510        {
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513            "aliases": [
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516            "file_set_type": "experimental data",
517            "lab": {
518                "title": "Ryan Corces, Gladstone Institute UCSF"
519            },
520            "preferred_assay_title": "10x multiome",
521            "status": "preview",
522            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
523        }
524    ],
525    "institutional_certificates": [
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527            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
528            "certificate_identifier": "IP115-05",
529            "controlled_access": false,
530            "status": "in progress"
531        }
532    ],
533    "lab": {
534        "@id": "/labs/ryan-corces/",
535        "title": "Ryan Corces, Gladstone Institute UCSF"
536    },
537    "lower_bound_age": 78,
538    "lower_bound_age_in_hours": 683280,
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603            "status": "preview"
604        },
605        {
606            "@id": "/multiplexed-samples/IGVFSM3192MEUT/",
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609        },
610        {
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613            "status": "preview"
614        },
615        {
616            "@id": "/multiplexed-samples/IGVFSM0496VQZI/",
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618            "status": "preview"
619        }
620    ],
621    "origin_of": [],
622    "parts": [],
623    "pmi": 198,
624    "pmi_units": "minute",
625    "pooled_in": [],
626    "preservation_method": "flash-freezing",
627    "protocols": [
628        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
629    ],
630    "sample_terms": [
631        {
632            "@id": "/sample-terms/UBERON_0002038/",
633            "status": "preview",
634            "term_name": "substantia nigra"
635        }
636    ],
637    "schema_version": "21",
638    "sex": "male",
639    "sorted_fractions": [],
640    "sources": [
641        {
642            "@id": "/sources/banner-health/",
643            "status": "released",
644            "title": "Banner Health"
645        }
646    ],
647    "status": "preview",
648    "submitted_by": {
649        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
650        "title": "Ryan Corces"
651    },
652    "summary": "Homo sapiens (male, 78 years) substantia nigra tissue associated with Parkinson's disease, mild cognitive impairment",
653    "taxa": "Homo sapiens",
654    "upper_bound_age": 78,
655    "upper_bound_age_in_hours": 683280,
656    "uuid": "2ae0f887-f561-45ce-b420-2cab7f67289d",
657    "virtual": false
658}