putamen — IGVFSM4780OQFA

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM4780OQFA/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM4780OQFA",
11    "age": "73",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN1570_PUT"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM4780OQFA](/tissues/IGVFSM4780OQFA/) has in progress subobject phenotype term [DOID_0080832](/phenotype-terms/DOID_0080832/).",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_item_status",
24                "path": "/tissues/IGVFSM4780OQFA/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM4780OQFA](/tissues/IGVFSM4780OQFA/) 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/IGVFSM4780OQFA/"
33            },
34            {
35                "category": "mismatched status",
36                "detail": "Preview tissue [IGVFSM4780OQFA](/tissues/IGVFSM4780OQFA/) 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/IGVFSM4780OQFA/"
41            },
42            {
43                "category": "missing CCF ID",
44                "detail": "Tissue [IGVFSM4780OQFA](/tissues/IGVFSM4780OQFA/) 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/IGVFSM4780OQFA/"
49            }
50        ]
51    },
52    "award": {
53        "@id": "/awards/HG012076/",
54        "component": "mapping"
55    },
56    "classifications": [
57        "tissue"
58    ],
59    "creation_timestamp": "2025-03-19T04:15:01.604602+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/IGVFDO7606UOXI/",
81            "accession": "IGVFDO7606UOXI",
82            "ethnicities": [
83                "European"
84            ],
85            "status": "preview"
86        }
87    ],
88    "file_sets": [
89        {
90            "@id": "/measurement-sets/IGVFDS2538KOXA/",
91            "accession": "IGVFDS2538KOXA",
92            "aliases": [
93                "igvf:corces_measurementSet_X044_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/IGVFDS0368CEBZ/",
105            "accession": "IGVFDS0368CEBZ",
106            "aliases": [
107                "igvf:corces_measurementSet_X044_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/IGVFDS4771HOQV/",
119            "accession": "IGVFDS4771HOQV",
120            "aliases": [
121                "igvf:corces_measurementSet_X044_G4_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/IGVFDS7058NUBI/",
133            "accession": "IGVFDS7058NUBI",
134            "aliases": [
135                "igvf:corces_measurementSet_X044_G4_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/IGVFDS8318EODY/",
147            "accession": "IGVFDS8318EODY",
148            "aliases": [
149                "igvf:corces_measurementSet_X044_G2_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/IGVFDS8707VRYD/",
161            "accession": "IGVFDS8707VRYD",
162            "aliases": [
163                "igvf:corces_measurementSet_X044_G2_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/IGVFDS5287UBUV/",
175            "accession": "IGVFDS5287UBUV",
176            "aliases": [
177                "igvf:corces_measurementSet_X044_G3_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/IGVFDS5812GPDP/",
189            "accession": "IGVFDS5812GPDP",
190            "aliases": [
191                "igvf:corces_measurementSet_X044_G3_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/IGVFDS1841XXQV/",
203            "accession": "IGVFDS1841XXQV",
204            "aliases": [
205                "igvf:corces_measurementSet_X044_G5_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/IGVFDS0168ULCR/",
217            "accession": "IGVFDS0168ULCR",
218            "aliases": [
219                "igvf:corces_measurementSet_X044_G5_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/IGVFDS3353QGFY/",
231            "accession": "IGVFDS3353QGFY",
232            "aliases": [
233                "igvf:corces_measurementSet_X044_G6_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/IGVFDS2747QBYZ/",
245            "accession": "IGVFDS2747QBYZ",
246            "aliases": [
247                "igvf:corces_measurementSet_X044_G6_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/IGVFDS1480DIMC/",
259            "accession": "IGVFDS1480DIMC",
260            "aliases": [
261                "igvf:corces_measurementSet_X044_G1_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/IGVFDS8295KFHG/",
273            "accession": "IGVFDS8295KFHG",
274            "aliases": [
275                "igvf:corces_measurementSet_X044_G1_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/IGVFDS3077XHHL/",
287            "accession": "IGVFDS3077XHHL",
288            "aliases": [
289                "igvf:corces_measurementSet_X044_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/IGVFDS6506DNXD/",
301            "accession": "IGVFDS6506DNXD",
302            "aliases": [
303                "igvf:corces_measurementSet_X044_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/IGVFDS8859FDEI/",
315            "accession": "IGVFDS8859FDEI",
316            "aliases": [
317                "igvf:corces_measurementSet_RP015_G2_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/IGVFDS9670KNNR/",
329            "accession": "IGVFDS9670KNNR",
330            "aliases": [
331                "igvf:corces_measurementSet_RP015_G2_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/IGVFDS1451RVGA/",
343            "accession": "IGVFDS1451RVGA",
344            "aliases": [
345                "igvf:corces_measurementSet_RP015_G3_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/IGVFDS0488NVQB/",
357            "accession": "IGVFDS0488NVQB",
358            "aliases": [
359                "igvf:corces_measurementSet_RP015_G3_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/IGVFDS0737RQRG/",
371            "accession": "IGVFDS0737RQRG",
372            "aliases": [
373                "igvf:corces_measurementSet_RP015_G4_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/IGVFDS7340HYVJ/",
385            "accession": "IGVFDS7340HYVJ",
386            "aliases": [
387                "igvf:corces_measurementSet_RP015_G4_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/IGVFDS9379ZJGH/",
399            "accession": "IGVFDS9379ZJGH",
400            "aliases": [
401                "igvf:corces_measurementSet_RP015_G1_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/IGVFDS2939KDMY/",
413            "accession": "IGVFDS2939KDMY",
414            "aliases": [
415                "igvf:corces_measurementSet_RP015_G1_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    "institutional_certificates": [
427        {
428            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
429            "certificate_identifier": "IP115-05",
430            "controlled_access": false,
431            "status": "in progress"
432        }
433    ],
434    "lab": {
435        "@id": "/labs/ryan-corces/",
436        "title": "Ryan Corces, Gladstone Institute UCSF"
437    },
438    "lower_bound_age": 73,
439    "lower_bound_age_in_hours": 639480,
440    "multiplexed_in": [
441        {
442            "@id": "/multiplexed-samples/IGVFSM7413MASU/",
443            "accession": "IGVFSM7413MASU",
444            "status": "preview"
445        },
446        {
447            "@id": "/multiplexed-samples/IGVFSM1493GMEH/",
448            "accession": "IGVFSM1493GMEH",
449            "status": "preview"
450        },
451        {
452            "@id": "/multiplexed-samples/IGVFSM6240XBPL/",
453            "accession": "IGVFSM6240XBPL",
454            "status": "preview"
455        },
456        {
457            "@id": "/multiplexed-samples/IGVFSM7680WXDX/",
458            "accession": "IGVFSM7680WXDX",
459            "status": "preview"
460        },
461        {
462            "@id": "/multiplexed-samples/IGVFSM1837EZTB/",
463            "accession": "IGVFSM1837EZTB",
464            "status": "preview"
465        },
466        {
467            "@id": "/multiplexed-samples/IGVFSM3425YHKS/",
468            "accession": "IGVFSM3425YHKS",
469            "status": "preview"
470        },
471        {
472            "@id": "/multiplexed-samples/IGVFSM2720AOAW/",
473            "accession": "IGVFSM2720AOAW",
474            "status": "preview"
475        },
476        {
477            "@id": "/multiplexed-samples/IGVFSM3090RRWU/",
478            "accession": "IGVFSM3090RRWU",
479            "status": "preview"
480        },
481        {
482            "@id": "/multiplexed-samples/IGVFSM3324TBYQ/",
483            "accession": "IGVFSM3324TBYQ",
484            "status": "preview"
485        },
486        {
487            "@id": "/multiplexed-samples/IGVFSM0903NROD/",
488            "accession": "IGVFSM0903NROD",
489            "status": "preview"
490        },
491        {
492            "@id": "/multiplexed-samples/IGVFSM0218TRNG/",
493            "accession": "IGVFSM0218TRNG",
494            "status": "preview"
495        },
496        {
497            "@id": "/multiplexed-samples/IGVFSM1969WJDB/",
498            "accession": "IGVFSM1969WJDB",
499            "status": "preview"
500        }
501    ],
502    "origin_of": [],
503    "parts": [],
504    "pmi": 352,
505    "pmi_units": "minute",
506    "pooled_in": [],
507    "preservation_method": "flash-freezing",
508    "protocols": [
509        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
510    ],
511    "sample_terms": [
512        {
513            "@id": "/sample-terms/UBERON_0001874/",
514            "status": "preview",
515            "term_name": "putamen"
516        }
517    ],
518    "schema_version": "21",
519    "sex": "male",
520    "sorted_fractions": [],
521    "sources": [
522        {
523            "@id": "/sources/banner-health/",
524            "status": "released",
525            "title": "Banner Health"
526        }
527    ],
528    "status": "preview",
529    "submitted_by": {
530        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
531        "title": "Ryan Corces"
532    },
533    "summary": "Homo sapiens (male, 73 years) putamen tissue associated with Parkinson's disease, cerebral amyloid angiopathy, mild cognitive impairment",
534    "taxa": "Homo sapiens",
535    "upper_bound_age": 73,
536    "upper_bound_age_in_hours": 639480,
537    "uuid": "86c16ac8-1c9c-4287-8b20-8aba58036617",
538    "virtual": false
539}