putamen — IGVFSM0545OFMV

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM0545OFMV/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM0545OFMV",
11    "age": "80",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1089_PUT"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM0545OFMV](/tissues/IGVFSM0545OFMV/) has in progress subobject phenotype term [DOID_9246](/phenotype-terms/DOID_9246/).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_item_status",
24                "path": "/tissues/IGVFSM0545OFMV/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM0545OFMV](/tissues/IGVFSM0545OFMV/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_item_status",
32                "path": "/tissues/IGVFSM0545OFMV/"
33            },
34            {
35                "category": "mismatched status",
36                "detail": "Preview tissue [IGVFSM0545OFMV](/tissues/IGVFSM0545OFMV/) 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/IGVFSM0545OFMV/"
41            },
42            {
43                "category": "missing CCF ID",
44                "detail": "Tissue [IGVFSM0545OFMV](/tissues/IGVFSM0545OFMV/) 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/IGVFSM0545OFMV/"
49            }
50        ]
51    },
52    "award": {
53        "@id": "/awards/HG012076/",
54        "component": "mapping"
55    },
56    "classifications": [
57        "tissue"
58    ],
59    "creation_timestamp": "2025-03-19T04:15:22.878351+00:00",
60    "date_obtained": "2023-03-16",
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/IGVFDO7315DYIP/",
81            "accession": "IGVFDO7315DYIP",
82            "ethnicities": [
83                "European"
84            ],
85            "status": "preview"
86        }
87    ],
88    "file_sets": [
89        {
90            "@id": "/measurement-sets/IGVFDS5765IJZT/",
91            "accession": "IGVFDS5765IJZT",
92            "aliases": [
93                "igvf:corces_measurementSet_X046_G7_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/IGVFDS6023ZQUI/",
105            "accession": "IGVFDS6023ZQUI",
106            "aliases": [
107                "igvf:corces_measurementSet_X046_G7_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/IGVFDS7624FKBF/",
119            "accession": "IGVFDS7624FKBF",
120            "aliases": [
121                "igvf:corces_measurementSet_X046_G8_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/IGVFDS0394LTRL/",
133            "accession": "IGVFDS0394LTRL",
134            "aliases": [
135                "igvf:corces_measurementSet_X046_G8_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/IGVFDS8203AABC/",
147            "accession": "IGVFDS8203AABC",
148            "aliases": [
149                "igvf:corces_measurementSet_X046_G4_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/IGVFDS5259BNNW/",
161            "accession": "IGVFDS5259BNNW",
162            "aliases": [
163                "igvf:corces_measurementSet_X046_G4_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/IGVFDS7287FFPC/",
175            "accession": "IGVFDS7287FFPC",
176            "aliases": [
177                "igvf:corces_measurementSet_X046_G2_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/IGVFDS0455TEQC/",
189            "accession": "IGVFDS0455TEQC",
190            "aliases": [
191                "igvf:corces_measurementSet_X046_G2_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/IGVFDS3046IPKB/",
203            "accession": "IGVFDS3046IPKB",
204            "aliases": [
205                "igvf:corces_measurementSet_X046_G3_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/IGVFDS5369HKHB/",
217            "accession": "IGVFDS5369HKHB",
218            "aliases": [
219                "igvf:corces_measurementSet_X046_G3_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/IGVFDS5773AVMD/",
231            "accession": "IGVFDS5773AVMD",
232            "aliases": [
233                "igvf:corces_measurementSet_X046_G5_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/IGVFDS4263YTZD/",
245            "accession": "IGVFDS4263YTZD",
246            "aliases": [
247                "igvf:corces_measurementSet_X046_G5_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/IGVFDS3724MEFH/",
259            "accession": "IGVFDS3724MEFH",
260            "aliases": [
261                "igvf:corces_measurementSet_X046_G6_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/IGVFDS6982QELB/",
273            "accession": "IGVFDS6982QELB",
274            "aliases": [
275                "igvf:corces_measurementSet_X046_G6_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/IGVFDS4582DKSD/",
287            "accession": "IGVFDS4582DKSD",
288            "aliases": [
289                "igvf:corces_measurementSet_X046_G1_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/IGVFDS7160XHZT/",
301            "accession": "IGVFDS7160XHZT",
302            "aliases": [
303                "igvf:corces_measurementSet_X046_G1_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    "institutional_certificates": [
315        {
316            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
317            "certificate_identifier": "IP115-05",
318            "controlled_access": false,
319            "status": "in progress"
320        }
321    ],
322    "lab": {
323        "@id": "/labs/ryan-corces/",
324        "title": "Ryan Corces, Gladstone Institute UCSF"
325    },
326    "lower_bound_age": 80,
327    "lower_bound_age_in_hours": 700800,
328    "multiplexed_in": [
329        {
330            "@id": "/multiplexed-samples/IGVFSM5223WGIQ/",
331            "accession": "IGVFSM5223WGIQ",
332            "status": "preview"
333        },
334        {
335            "@id": "/multiplexed-samples/IGVFSM3471DKMI/",
336            "accession": "IGVFSM3471DKMI",
337            "status": "preview"
338        },
339        {
340            "@id": "/multiplexed-samples/IGVFSM6731GWSI/",
341            "accession": "IGVFSM6731GWSI",
342            "status": "preview"
343        },
344        {
345            "@id": "/multiplexed-samples/IGVFSM7324LMEY/",
346            "accession": "IGVFSM7324LMEY",
347            "status": "preview"
348        },
349        {
350            "@id": "/multiplexed-samples/IGVFSM5266CSDR/",
351            "accession": "IGVFSM5266CSDR",
352            "status": "preview"
353        },
354        {
355            "@id": "/multiplexed-samples/IGVFSM2300MKEN/",
356            "accession": "IGVFSM2300MKEN",
357            "status": "preview"
358        },
359        {
360            "@id": "/multiplexed-samples/IGVFSM4792JPXR/",
361            "accession": "IGVFSM4792JPXR",
362            "status": "preview"
363        },
364        {
365            "@id": "/multiplexed-samples/IGVFSM2825UXQB/",
366            "accession": "IGVFSM2825UXQB",
367            "status": "preview"
368        }
369    ],
370    "origin_of": [],
371    "parts": [],
372    "pmi": 195,
373    "pmi_units": "minute",
374    "pooled_in": [],
375    "preservation_method": "flash-freezing",
376    "protocols": [
377        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
378    ],
379    "sample_terms": [
380        {
381            "@id": "/sample-terms/UBERON_0001874/",
382            "status": "preview",
383            "term_name": "putamen"
384        }
385    ],
386    "schema_version": "21",
387    "sex": "female",
388    "sorted_fractions": [],
389    "sources": [
390        {
391            "@id": "/sources/banner-health/",
392            "status": "released",
393            "title": "Banner Health"
394        }
395    ],
396    "status": "preview",
397    "submitted_by": {
398        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
399        "title": "Ryan Corces"
400    },
401    "summary": "Homo sapiens (female, 80 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
402    "taxa": "Homo sapiens",
403    "upper_bound_age": 80,
404    "upper_bound_age_in_hours": 700800,
405    "uuid": "8d20fdca-10da-430b-a8f9-aec06a9eaaed",
406    "virtual": false
407}