substantia nigra — IGVFSM1248IPGG

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM1248IPGG/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM1248IPGG",
11    "age": "82",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN0437_SN"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM1248IPGG](/tissues/IGVFSM1248IPGG/) has in progress subobject phenotype term [DOID_2377](/phenotype-terms/DOID_2377/).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_item_status",
24                "path": "/tissues/IGVFSM1248IPGG/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM1248IPGG](/tissues/IGVFSM1248IPGG/) 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/IGVFSM1248IPGG/"
33            },
34            {
35                "category": "mismatched status",
36                "detail": "Preview tissue [IGVFSM1248IPGG](/tissues/IGVFSM1248IPGG/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
37                "level": 30,
38                "level_name": "INTERNAL_ACTION",
39                "name": "audit_item_status",
40                "path": "/tissues/IGVFSM1248IPGG/"
41            },
42            {
43                "category": "missing CCF ID",
44                "detail": "Tissue [IGVFSM1248IPGG](/tissues/IGVFSM1248IPGG/) 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/IGVFSM1248IPGG/"
49            }
50        ]
51    },
52    "award": {
53        "@id": "/awards/HG012076/",
54        "component": "mapping"
55    },
56    "classifications": [
57        "tissue"
58    ],
59    "creation_timestamp": "2025-03-19T04:14:28.998660+00:00",
60    "date_obtained": "2023-03-07",
61    "disease_terms": [
62        {
63            "@id": "/phenotype-terms/MONDO_0004975/",
64            "status": "released",
65            "term_name": "Alzheimer disease"
66        },
67        {
68            "@id": "/phenotype-terms/DOID_14330/",
69            "status": "in progress",
70            "term_name": "Parkinson's disease"
71        },
72        {
73            "@id": "/phenotype-terms/DOID_9246/",
74            "status": "in progress",
75            "term_name": "cerebral amyloid angiopathy"
76        },
77        {
78            "@id": "/phenotype-terms/DOID_2377/",
79            "status": "in progress",
80            "term_name": "multiple sclerosis"
81        }
82    ],
83    "donors": [
84        {
85            "@id": "/human-donors/IGVFDO8155MCUV/",
86            "accession": "IGVFDO8155MCUV",
87            "ethnicities": [
88                "European"
89            ],
90            "status": "preview"
91        }
92    ],
93    "file_sets": [
94        {
95            "@id": "/measurement-sets/IGVFDS6077CQVA/",
96            "accession": "IGVFDS6077CQVA",
97            "aliases": [
98                "igvf:corces_measurementSet_X041_G6_ATAC"
99            ],
100            "file_set_type": "experimental data",
101            "lab": {
102                "title": "Ryan Corces, Gladstone Institute UCSF"
103            },
104            "preferred_assay_title": "10x multiome",
105            "status": "preview",
106            "summary": "single-nucleus ATAC-seq (10x multiome)"
107        },
108        {
109            "@id": "/measurement-sets/IGVFDS5006HOVG/",
110            "accession": "IGVFDS5006HOVG",
111            "aliases": [
112                "igvf:corces_measurementSet_X041_G6_RNA"
113            ],
114            "file_set_type": "experimental data",
115            "lab": {
116                "title": "Ryan Corces, Gladstone Institute UCSF"
117            },
118            "preferred_assay_title": "10x multiome",
119            "status": "preview",
120            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
121        },
122        {
123            "@id": "/measurement-sets/IGVFDS3083RFCQ/",
124            "accession": "IGVFDS3083RFCQ",
125            "aliases": [
126                "igvf:corces_measurementSet_X041_G1_ATAC"
127            ],
128            "file_set_type": "experimental data",
129            "lab": {
130                "title": "Ryan Corces, Gladstone Institute UCSF"
131            },
132            "preferred_assay_title": "10x multiome",
133            "status": "preview",
134            "summary": "single-nucleus ATAC-seq (10x multiome)"
135        },
136        {
137            "@id": "/measurement-sets/IGVFDS1691KPWU/",
138            "accession": "IGVFDS1691KPWU",
139            "aliases": [
140                "igvf:corces_measurementSet_X041_G1_RNA"
141            ],
142            "file_set_type": "experimental data",
143            "lab": {
144                "title": "Ryan Corces, Gladstone Institute UCSF"
145            },
146            "preferred_assay_title": "10x multiome",
147            "status": "preview",
148            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
149        },
150        {
151            "@id": "/measurement-sets/IGVFDS9809VXKU/",
152            "accession": "IGVFDS9809VXKU",
153            "aliases": [
154                "igvf:corces_measurementSet_X041_G3_ATAC"
155            ],
156            "file_set_type": "experimental data",
157            "lab": {
158                "title": "Ryan Corces, Gladstone Institute UCSF"
159            },
160            "preferred_assay_title": "10x multiome",
161            "status": "preview",
162            "summary": "single-nucleus ATAC-seq (10x multiome)"
163        },
164        {
165            "@id": "/measurement-sets/IGVFDS6769MHJX/",
166            "accession": "IGVFDS6769MHJX",
167            "aliases": [
168                "igvf:corces_measurementSet_X041_G3_RNA"
169            ],
170            "file_set_type": "experimental data",
171            "lab": {
172                "title": "Ryan Corces, Gladstone Institute UCSF"
173            },
174            "preferred_assay_title": "10x multiome",
175            "status": "preview",
176            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
177        },
178        {
179            "@id": "/measurement-sets/IGVFDS5236WFMM/",
180            "accession": "IGVFDS5236WFMM",
181            "aliases": [
182                "igvf:corces_measurementSet_X041_G2_ATAC"
183            ],
184            "file_set_type": "experimental data",
185            "lab": {
186                "title": "Ryan Corces, Gladstone Institute UCSF"
187            },
188            "preferred_assay_title": "10x multiome",
189            "status": "preview",
190            "summary": "single-nucleus ATAC-seq (10x multiome)"
191        },
192        {
193            "@id": "/measurement-sets/IGVFDS8913NULI/",
194            "accession": "IGVFDS8913NULI",
195            "aliases": [
196                "igvf:corces_measurementSet_X041_G2_RNA"
197            ],
198            "file_set_type": "experimental data",
199            "lab": {
200                "title": "Ryan Corces, Gladstone Institute UCSF"
201            },
202            "preferred_assay_title": "10x multiome",
203            "status": "preview",
204            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
205        },
206        {
207            "@id": "/measurement-sets/IGVFDS7843JHRO/",
208            "accession": "IGVFDS7843JHRO",
209            "aliases": [
210                "igvf:corces_measurementSet_X041_G4_ATAC"
211            ],
212            "file_set_type": "experimental data",
213            "lab": {
214                "title": "Ryan Corces, Gladstone Institute UCSF"
215            },
216            "preferred_assay_title": "10x multiome",
217            "status": "preview",
218            "summary": "single-nucleus ATAC-seq (10x multiome)"
219        },
220        {
221            "@id": "/measurement-sets/IGVFDS7314VGYF/",
222            "accession": "IGVFDS7314VGYF",
223            "aliases": [
224                "igvf:corces_measurementSet_X041_G4_RNA"
225            ],
226            "file_set_type": "experimental data",
227            "lab": {
228                "title": "Ryan Corces, Gladstone Institute UCSF"
229            },
230            "preferred_assay_title": "10x multiome",
231            "status": "preview",
232            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
233        },
234        {
235            "@id": "/measurement-sets/IGVFDS4454OQTQ/",
236            "accession": "IGVFDS4454OQTQ",
237            "aliases": [
238                "igvf:corces_measurementSet_X041_G7_ATAC"
239            ],
240            "file_set_type": "experimental data",
241            "lab": {
242                "title": "Ryan Corces, Gladstone Institute UCSF"
243            },
244            "preferred_assay_title": "10x multiome",
245            "status": "preview",
246            "summary": "single-nucleus ATAC-seq (10x multiome)"
247        },
248        {
249            "@id": "/measurement-sets/IGVFDS3636ZYTF/",
250            "accession": "IGVFDS3636ZYTF",
251            "aliases": [
252                "igvf:corces_measurementSet_X041_G7_RNA"
253            ],
254            "file_set_type": "experimental data",
255            "lab": {
256                "title": "Ryan Corces, Gladstone Institute UCSF"
257            },
258            "preferred_assay_title": "10x multiome",
259            "status": "preview",
260            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
261        },
262        {
263            "@id": "/measurement-sets/IGVFDS5800WXVK/",
264            "accession": "IGVFDS5800WXVK",
265            "aliases": [
266                "igvf:corces_measurementSet_X041_G5_ATAC"
267            ],
268            "file_set_type": "experimental data",
269            "lab": {
270                "title": "Ryan Corces, Gladstone Institute UCSF"
271            },
272            "preferred_assay_title": "10x multiome",
273            "status": "preview",
274            "summary": "single-nucleus ATAC-seq (10x multiome)"
275        },
276        {
277            "@id": "/measurement-sets/IGVFDS2612AYOV/",
278            "accession": "IGVFDS2612AYOV",
279            "aliases": [
280                "igvf:corces_measurementSet_X041_G5_RNA"
281            ],
282            "file_set_type": "experimental data",
283            "lab": {
284                "title": "Ryan Corces, Gladstone Institute UCSF"
285            },
286            "preferred_assay_title": "10x multiome",
287            "status": "preview",
288            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
289        },
290        {
291            "@id": "/measurement-sets/IGVFDS0738WMFX/",
292            "accession": "IGVFDS0738WMFX",
293            "aliases": [
294                "igvf:corces_measurementSet_X041_G8_RNA"
295            ],
296            "file_set_type": "experimental data",
297            "lab": {
298                "title": "Ryan Corces, Gladstone Institute UCSF"
299            },
300            "preferred_assay_title": "10x multiome",
301            "status": "preview",
302            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
303        },
304        {
305            "@id": "/measurement-sets/IGVFDS9587VFRN/",
306            "accession": "IGVFDS9587VFRN",
307            "aliases": [
308                "igvf:corces_measurementSet_X041_G8_ATAC"
309            ],
310            "file_set_type": "experimental data",
311            "lab": {
312                "title": "Ryan Corces, Gladstone Institute UCSF"
313            },
314            "preferred_assay_title": "10x multiome",
315            "status": "preview",
316            "summary": "single-nucleus ATAC-seq (10x multiome)"
317        }
318    ],
319    "institutional_certificates": [
320        {
321            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
322            "certificate_identifier": "IP115-05",
323            "controlled_access": false,
324            "status": "in progress"
325        }
326    ],
327    "lab": {
328        "@id": "/labs/ryan-corces/",
329        "title": "Ryan Corces, Gladstone Institute UCSF"
330    },
331    "lower_bound_age": 82,
332    "lower_bound_age_in_hours": 718320,
333    "multiplexed_in": [
334        {
335            "@id": "/multiplexed-samples/IGVFSM0027DAWZ/",
336            "accession": "IGVFSM0027DAWZ",
337            "status": "preview"
338        },
339        {
340            "@id": "/multiplexed-samples/IGVFSM1990PUGQ/",
341            "accession": "IGVFSM1990PUGQ",
342            "status": "preview"
343        },
344        {
345            "@id": "/multiplexed-samples/IGVFSM5674WWIP/",
346            "accession": "IGVFSM5674WWIP",
347            "status": "preview"
348        },
349        {
350            "@id": "/multiplexed-samples/IGVFSM6363AZVN/",
351            "accession": "IGVFSM6363AZVN",
352            "status": "preview"
353        },
354        {
355            "@id": "/multiplexed-samples/IGVFSM0728SZZR/",
356            "accession": "IGVFSM0728SZZR",
357            "status": "preview"
358        },
359        {
360            "@id": "/multiplexed-samples/IGVFSM8345ETIT/",
361            "accession": "IGVFSM8345ETIT",
362            "status": "preview"
363        },
364        {
365            "@id": "/multiplexed-samples/IGVFSM4462GKQC/",
366            "accession": "IGVFSM4462GKQC",
367            "status": "preview"
368        },
369        {
370            "@id": "/multiplexed-samples/IGVFSM3938LXBP/",
371            "accession": "IGVFSM3938LXBP",
372            "status": "preview"
373        }
374    ],
375    "origin_of": [],
376    "parts": [],
377    "pmi": 135,
378    "pmi_units": "minute",
379    "pooled_in": [],
380    "preservation_method": "flash-freezing",
381    "protocols": [
382        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
383    ],
384    "sample_terms": [
385        {
386            "@id": "/sample-terms/UBERON_0002038/",
387            "status": "preview",
388            "term_name": "substantia nigra"
389        }
390    ],
391    "schema_version": "21",
392    "sex": "female",
393    "sorted_fractions": [],
394    "sources": [
395        {
396            "@id": "/sources/banner-health/",
397            "status": "released",
398            "title": "Banner Health"
399        }
400    ],
401    "status": "preview",
402    "submitted_by": {
403        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
404        "title": "Ryan Corces"
405    },
406    "summary": "Homo sapiens (female, 82 years) substantia nigra tissue associated with Alzheimer disease, Parkinson's disease, cerebral amyloid angiopathy, multiple sclerosis",
407    "taxa": "Homo sapiens",
408    "upper_bound_age": 82,
409    "upper_bound_age_in_hours": 718320,
410    "uuid": "16290038-1c3c-4b90-ad1d-ca2dd1cc50a4",
411    "virtual": false
412}