putamen — IGVFSM9425DRXU

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM9425DRXU/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM9425DRXU",
11    "age": "80",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN0129_PUT"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM9425DRXU](/tissues/IGVFSM9425DRXU/) 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/IGVFSM9425DRXU/"
25            },
26            {
27                "category": "mismatched status",
28                "detail": "Preview tissue [IGVFSM9425DRXU](/tissues/IGVFSM9425DRXU/) 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/IGVFSM9425DRXU/"
33            },
34            {
35                "category": "missing CCF ID",
36                "detail": "Tissue [IGVFSM9425DRXU](/tissues/IGVFSM9425DRXU/) 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/IGVFSM9425DRXU/"
41            }
42        ]
43    },
44    "award": {
45        "@id": "/awards/HG012076/",
46        "component": "mapping"
47    },
48    "classifications": [
49        "tissue"
50    ],
51    "creation_timestamp": "2025-03-19T04:14:04.878120+00:00",
52    "date_obtained": "2023-02-22",
53    "disease_terms": [
54        {
55            "@id": "/phenotype-terms/MONDO_0004975/",
56            "status": "released",
57            "term_name": "Alzheimer disease"
58        },
59        {
60            "@id": "/phenotype-terms/DOID_14330/",
61            "status": "in progress",
62            "term_name": "Parkinson's disease"
63        },
64        {
65            "@id": "/phenotype-terms/DOID_9246/",
66            "status": "in progress",
67            "term_name": "cerebral amyloid angiopathy"
68        }
69    ],
70    "donors": [
71        {
72            "@id": "/human-donors/IGVFDO4191KJBR/",
73            "accession": "IGVFDO4191KJBR",
74            "ethnicities": [
75                "European"
76            ],
77            "status": "preview"
78        }
79    ],
80    "file_sets": [
81        {
82            "@id": "/measurement-sets/IGVFDS5733DNRB/",
83            "accession": "IGVFDS5733DNRB",
84            "aliases": [
85                "igvf:corces_measurementSet_X040_G7_ATAC"
86            ],
87            "file_set_type": "experimental data",
88            "lab": {
89                "title": "Ryan Corces, Gladstone Institute UCSF"
90            },
91            "preferred_assay_title": "10x multiome",
92            "status": "preview",
93            "summary": "single-nucleus ATAC-seq (10x multiome)"
94        },
95        {
96            "@id": "/measurement-sets/IGVFDS8796ZGJG/",
97            "accession": "IGVFDS8796ZGJG",
98            "aliases": [
99                "igvf:corces_measurementSet_X040_G7_RNA"
100            ],
101            "file_set_type": "experimental data",
102            "lab": {
103                "title": "Ryan Corces, Gladstone Institute UCSF"
104            },
105            "preferred_assay_title": "10x multiome",
106            "status": "preview",
107            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
108        },
109        {
110            "@id": "/measurement-sets/IGVFDS1992IYHH/",
111            "accession": "IGVFDS1992IYHH",
112            "aliases": [
113                "igvf:corces_measurementSet_X040_G3_ATAC"
114            ],
115            "file_set_type": "experimental data",
116            "lab": {
117                "title": "Ryan Corces, Gladstone Institute UCSF"
118            },
119            "preferred_assay_title": "10x multiome",
120            "status": "preview",
121            "summary": "single-nucleus ATAC-seq (10x multiome)"
122        },
123        {
124            "@id": "/measurement-sets/IGVFDS8031ICKM/",
125            "accession": "IGVFDS8031ICKM",
126            "aliases": [
127                "igvf:corces_measurementSet_X040_G3_RNA"
128            ],
129            "file_set_type": "experimental data",
130            "lab": {
131                "title": "Ryan Corces, Gladstone Institute UCSF"
132            },
133            "preferred_assay_title": "10x multiome",
134            "status": "preview",
135            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
136        },
137        {
138            "@id": "/measurement-sets/IGVFDS5414UFNC/",
139            "accession": "IGVFDS5414UFNC",
140            "aliases": [
141                "igvf:corces_measurementSet_X040_G1_ATAC"
142            ],
143            "file_set_type": "experimental data",
144            "lab": {
145                "title": "Ryan Corces, Gladstone Institute UCSF"
146            },
147            "preferred_assay_title": "10x multiome",
148            "status": "preview",
149            "summary": "single-nucleus ATAC-seq (10x multiome)"
150        },
151        {
152            "@id": "/measurement-sets/IGVFDS2806EVXQ/",
153            "accession": "IGVFDS2806EVXQ",
154            "aliases": [
155                "igvf:corces_measurementSet_X040_G1_RNA"
156            ],
157            "file_set_type": "experimental data",
158            "lab": {
159                "title": "Ryan Corces, Gladstone Institute UCSF"
160            },
161            "preferred_assay_title": "10x multiome",
162            "status": "preview",
163            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
164        },
165        {
166            "@id": "/measurement-sets/IGVFDS1310RPDD/",
167            "accession": "IGVFDS1310RPDD",
168            "aliases": [
169                "igvf:corces_measurementSet_X040_G4_ATAC"
170            ],
171            "file_set_type": "experimental data",
172            "lab": {
173                "title": "Ryan Corces, Gladstone Institute UCSF"
174            },
175            "preferred_assay_title": "10x multiome",
176            "status": "preview",
177            "summary": "single-nucleus ATAC-seq (10x multiome)"
178        },
179        {
180            "@id": "/measurement-sets/IGVFDS9460DSVF/",
181            "accession": "IGVFDS9460DSVF",
182            "aliases": [
183                "igvf:corces_measurementSet_X040_G4_RNA"
184            ],
185            "file_set_type": "experimental data",
186            "lab": {
187                "title": "Ryan Corces, Gladstone Institute UCSF"
188            },
189            "preferred_assay_title": "10x multiome",
190            "status": "preview",
191            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
192        },
193        {
194            "@id": "/measurement-sets/IGVFDS3830MHQW/",
195            "accession": "IGVFDS3830MHQW",
196            "aliases": [
197                "igvf:corces_measurementSet_X040_G6_ATAC"
198            ],
199            "file_set_type": "experimental data",
200            "lab": {
201                "title": "Ryan Corces, Gladstone Institute UCSF"
202            },
203            "preferred_assay_title": "10x multiome",
204            "status": "preview",
205            "summary": "single-nucleus ATAC-seq (10x multiome)"
206        },
207        {
208            "@id": "/measurement-sets/IGVFDS4245QFMN/",
209            "accession": "IGVFDS4245QFMN",
210            "aliases": [
211                "igvf:corces_measurementSet_X040_G6_RNA"
212            ],
213            "file_set_type": "experimental data",
214            "lab": {
215                "title": "Ryan Corces, Gladstone Institute UCSF"
216            },
217            "preferred_assay_title": "10x multiome",
218            "status": "preview",
219            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
220        },
221        {
222            "@id": "/measurement-sets/IGVFDS8899IUPN/",
223            "accession": "IGVFDS8899IUPN",
224            "aliases": [
225                "igvf:corces_measurementSet_X040_G5_ATAC"
226            ],
227            "file_set_type": "experimental data",
228            "lab": {
229                "title": "Ryan Corces, Gladstone Institute UCSF"
230            },
231            "preferred_assay_title": "10x multiome",
232            "status": "preview",
233            "summary": "single-nucleus ATAC-seq (10x multiome)"
234        },
235        {
236            "@id": "/measurement-sets/IGVFDS4045ZVBI/",
237            "accession": "IGVFDS4045ZVBI",
238            "aliases": [
239                "igvf:corces_measurementSet_X040_G5_RNA"
240            ],
241            "file_set_type": "experimental data",
242            "lab": {
243                "title": "Ryan Corces, Gladstone Institute UCSF"
244            },
245            "preferred_assay_title": "10x multiome",
246            "status": "preview",
247            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
248        },
249        {
250            "@id": "/measurement-sets/IGVFDS2033BVMC/",
251            "accession": "IGVFDS2033BVMC",
252            "aliases": [
253                "igvf:corces_measurementSet_X040_G2_ATAC"
254            ],
255            "file_set_type": "experimental data",
256            "lab": {
257                "title": "Ryan Corces, Gladstone Institute UCSF"
258            },
259            "preferred_assay_title": "10x multiome",
260            "status": "preview",
261            "summary": "single-nucleus ATAC-seq (10x multiome)"
262        },
263        {
264            "@id": "/measurement-sets/IGVFDS7813FCIC/",
265            "accession": "IGVFDS7813FCIC",
266            "aliases": [
267                "igvf:corces_measurementSet_X040_G2_RNA"
268            ],
269            "file_set_type": "experimental data",
270            "lab": {
271                "title": "Ryan Corces, Gladstone Institute UCSF"
272            },
273            "preferred_assay_title": "10x multiome",
274            "status": "preview",
275            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
276        },
277        {
278            "@id": "/measurement-sets/IGVFDS8948WYQH/",
279            "accession": "IGVFDS8948WYQH",
280            "aliases": [
281                "igvf:corces_measurementSet_X040_G8_ATAC"
282            ],
283            "file_set_type": "experimental data",
284            "lab": {
285                "title": "Ryan Corces, Gladstone Institute UCSF"
286            },
287            "preferred_assay_title": "10x multiome",
288            "status": "preview",
289            "summary": "single-nucleus ATAC-seq (10x multiome)"
290        },
291        {
292            "@id": "/measurement-sets/IGVFDS1158PFBA/",
293            "accession": "IGVFDS1158PFBA",
294            "aliases": [
295                "igvf:corces_measurementSet_X040_G8_RNA"
296            ],
297            "file_set_type": "experimental data",
298            "lab": {
299                "title": "Ryan Corces, Gladstone Institute UCSF"
300            },
301            "preferred_assay_title": "10x multiome",
302            "status": "preview",
303            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
304        },
305        {
306            "@id": "/measurement-sets/IGVFDS2943LQHU/",
307            "accession": "IGVFDS2943LQHU",
308            "aliases": [
309                "igvf:corces_measurementSet_RP014_G3_ATAC"
310            ],
311            "file_set_type": "experimental data",
312            "lab": {
313                "title": "Ryan Corces, Gladstone Institute UCSF"
314            },
315            "preferred_assay_title": "10x multiome",
316            "status": "preview",
317            "summary": "single-nucleus ATAC-seq (10x multiome)"
318        },
319        {
320            "@id": "/measurement-sets/IGVFDS3707VRFM/",
321            "accession": "IGVFDS3707VRFM",
322            "aliases": [
323                "igvf:corces_measurementSet_RP014_G3_RNA"
324            ],
325            "file_set_type": "experimental data",
326            "lab": {
327                "title": "Ryan Corces, Gladstone Institute UCSF"
328            },
329            "preferred_assay_title": "10x multiome",
330            "status": "preview",
331            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
332        },
333        {
334            "@id": "/measurement-sets/IGVFDS7788KKVV/",
335            "accession": "IGVFDS7788KKVV",
336            "aliases": [
337                "igvf:corces_measurementSet_RP014_G2_ATAC"
338            ],
339            "file_set_type": "experimental data",
340            "lab": {
341                "title": "Ryan Corces, Gladstone Institute UCSF"
342            },
343            "preferred_assay_title": "10x multiome",
344            "status": "preview",
345            "summary": "single-nucleus ATAC-seq (10x multiome)"
346        },
347        {
348            "@id": "/measurement-sets/IGVFDS3071BBZO/",
349            "accession": "IGVFDS3071BBZO",
350            "aliases": [
351                "igvf:corces_measurementSet_RP014_G2_RNA"
352            ],
353            "file_set_type": "experimental data",
354            "lab": {
355                "title": "Ryan Corces, Gladstone Institute UCSF"
356            },
357            "preferred_assay_title": "10x multiome",
358            "status": "preview",
359            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
360        },
361        {
362            "@id": "/measurement-sets/IGVFDS3473OBBZ/",
363            "accession": "IGVFDS3473OBBZ",
364            "aliases": [
365                "igvf:corces_measurementSet_RP014_G8_RNA"
366            ],
367            "file_set_type": "experimental data",
368            "lab": {
369                "title": "Ryan Corces, Gladstone Institute UCSF"
370            },
371            "preferred_assay_title": "10x multiome",
372            "status": "preview",
373            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
374        },
375        {
376            "@id": "/measurement-sets/IGVFDS5184YEZB/",
377            "accession": "IGVFDS5184YEZB",
378            "aliases": [
379                "igvf:corces_measurementSet_RP014_G8_ATAC"
380            ],
381            "file_set_type": "experimental data",
382            "lab": {
383                "title": "Ryan Corces, Gladstone Institute UCSF"
384            },
385            "preferred_assay_title": "10x multiome",
386            "status": "preview",
387            "summary": "single-nucleus ATAC-seq (10x multiome)"
388        },
389        {
390            "@id": "/measurement-sets/IGVFDS5508ONPS/",
391            "accession": "IGVFDS5508ONPS",
392            "aliases": [
393                "igvf:corces_measurementSet_RP014_G4_ATAC"
394            ],
395            "file_set_type": "experimental data",
396            "lab": {
397                "title": "Ryan Corces, Gladstone Institute UCSF"
398            },
399            "preferred_assay_title": "10x multiome",
400            "status": "preview",
401            "summary": "single-nucleus ATAC-seq (10x multiome)"
402        },
403        {
404            "@id": "/measurement-sets/IGVFDS0058HQMM/",
405            "accession": "IGVFDS0058HQMM",
406            "aliases": [
407                "igvf:corces_measurementSet_RP014_G4_RNA"
408            ],
409            "file_set_type": "experimental data",
410            "lab": {
411                "title": "Ryan Corces, Gladstone Institute UCSF"
412            },
413            "preferred_assay_title": "10x multiome",
414            "status": "preview",
415            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
416        },
417        {
418            "@id": "/measurement-sets/IGVFDS3802KJSR/",
419            "accession": "IGVFDS3802KJSR",
420            "aliases": [
421                "igvf:corces_measurementSet_RP014_G5_ATAC"
422            ],
423            "file_set_type": "experimental data",
424            "lab": {
425                "title": "Ryan Corces, Gladstone Institute UCSF"
426            },
427            "preferred_assay_title": "10x multiome",
428            "status": "preview",
429            "summary": "single-nucleus ATAC-seq (10x multiome)"
430        },
431        {
432            "@id": "/measurement-sets/IGVFDS6353IHVX/",
433            "accession": "IGVFDS6353IHVX",
434            "aliases": [
435                "igvf:corces_measurementSet_RP014_G5_RNA"
436            ],
437            "file_set_type": "experimental data",
438            "lab": {
439                "title": "Ryan Corces, Gladstone Institute UCSF"
440            },
441            "preferred_assay_title": "10x multiome",
442            "status": "preview",
443            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
444        },
445        {
446            "@id": "/measurement-sets/IGVFDS9599ZHWG/",
447            "accession": "IGVFDS9599ZHWG",
448            "aliases": [
449                "igvf:corces_measurementSet_RP014_G1_ATAC"
450            ],
451            "file_set_type": "experimental data",
452            "lab": {
453                "title": "Ryan Corces, Gladstone Institute UCSF"
454            },
455            "preferred_assay_title": "10x multiome",
456            "status": "preview",
457            "summary": "single-nucleus ATAC-seq (10x multiome)"
458        },
459        {
460            "@id": "/measurement-sets/IGVFDS4610DVCB/",
461            "accession": "IGVFDS4610DVCB",
462            "aliases": [
463                "igvf:corces_measurementSet_RP014_G1_RNA"
464            ],
465            "file_set_type": "experimental data",
466            "lab": {
467                "title": "Ryan Corces, Gladstone Institute UCSF"
468            },
469            "preferred_assay_title": "10x multiome",
470            "status": "preview",
471            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
472        },
473        {
474            "@id": "/measurement-sets/IGVFDS0957VZJU/",
475            "accession": "IGVFDS0957VZJU",
476            "aliases": [
477                "igvf:corces_measurementSet_RP014_G6_ATAC"
478            ],
479            "file_set_type": "experimental data",
480            "lab": {
481                "title": "Ryan Corces, Gladstone Institute UCSF"
482            },
483            "preferred_assay_title": "10x multiome",
484            "status": "preview",
485            "summary": "single-nucleus ATAC-seq (10x multiome)"
486        },
487        {
488            "@id": "/measurement-sets/IGVFDS3998OHPZ/",
489            "accession": "IGVFDS3998OHPZ",
490            "aliases": [
491                "igvf:corces_measurementSet_RP014_G6_RNA"
492            ],
493            "file_set_type": "experimental data",
494            "lab": {
495                "title": "Ryan Corces, Gladstone Institute UCSF"
496            },
497            "preferred_assay_title": "10x multiome",
498            "status": "preview",
499            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
500        },
501        {
502            "@id": "/measurement-sets/IGVFDS6041FJHB/",
503            "accession": "IGVFDS6041FJHB",
504            "aliases": [
505                "igvf:corces_measurementSet_RP014_G7_ATAC"
506            ],
507            "file_set_type": "experimental data",
508            "lab": {
509                "title": "Ryan Corces, Gladstone Institute UCSF"
510            },
511            "preferred_assay_title": "10x multiome",
512            "status": "preview",
513            "summary": "single-nucleus ATAC-seq (10x multiome)"
514        },
515        {
516            "@id": "/measurement-sets/IGVFDS2731RLBA/",
517            "accession": "IGVFDS2731RLBA",
518            "aliases": [
519                "igvf:corces_measurementSet_RP014_G7_RNA"
520            ],
521            "file_set_type": "experimental data",
522            "lab": {
523                "title": "Ryan Corces, Gladstone Institute UCSF"
524            },
525            "preferred_assay_title": "10x multiome",
526            "status": "preview",
527            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
528        }
529    ],
530    "institutional_certificates": [
531        {
532            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
533            "certificate_identifier": "IP115-05",
534            "controlled_access": false,
535            "data_use_limitation_summary": "No limitations",
536            "status": "in progress"
537        }
538    ],
539    "lab": {
540        "@id": "/labs/ryan-corces/",
541        "title": "Ryan Corces, Gladstone Institute UCSF"
542    },
543    "lower_bound_age": 80,
544    "lower_bound_age_in_hours": 700800,
545    "multiplexed_in": [
546        {
547            "@id": "/multiplexed-samples/IGVFSM3718ZLPR/",
548            "accession": "IGVFSM3718ZLPR",
549            "status": "preview"
550        },
551        {
552            "@id": "/multiplexed-samples/IGVFSM1109QIDV/",
553            "accession": "IGVFSM1109QIDV",
554            "status": "preview"
555        },
556        {
557            "@id": "/multiplexed-samples/IGVFSM7243MOJZ/",
558            "accession": "IGVFSM7243MOJZ",
559            "status": "preview"
560        },
561        {
562            "@id": "/multiplexed-samples/IGVFSM1867DNXU/",
563            "accession": "IGVFSM1867DNXU",
564            "status": "preview"
565        },
566        {
567            "@id": "/multiplexed-samples/IGVFSM9187MAHV/",
568            "accession": "IGVFSM9187MAHV",
569            "status": "preview"
570        },
571        {
572            "@id": "/multiplexed-samples/IGVFSM6104DPZN/",
573            "accession": "IGVFSM6104DPZN",
574            "status": "preview"
575        },
576        {
577            "@id": "/multiplexed-samples/IGVFSM7690RNGC/",
578            "accession": "IGVFSM7690RNGC",
579            "status": "preview"
580        },
581        {
582            "@id": "/multiplexed-samples/IGVFSM7148SYPE/",
583            "accession": "IGVFSM7148SYPE",
584            "status": "preview"
585        },
586        {
587            "@id": "/multiplexed-samples/IGVFSM4901QTFI/",
588            "accession": "IGVFSM4901QTFI",
589            "status": "preview"
590        },
591        {
592            "@id": "/multiplexed-samples/IGVFSM7335HESV/",
593            "accession": "IGVFSM7335HESV",
594            "status": "preview"
595        },
596        {
597            "@id": "/multiplexed-samples/IGVFSM7659CCOT/",
598            "accession": "IGVFSM7659CCOT",
599            "status": "preview"
600        },
601        {
602            "@id": "/multiplexed-samples/IGVFSM8048XYHR/",
603            "accession": "IGVFSM8048XYHR",
604            "status": "preview"
605        },
606        {
607            "@id": "/multiplexed-samples/IGVFSM5142KRLD/",
608            "accession": "IGVFSM5142KRLD",
609            "status": "preview"
610        },
611        {
612            "@id": "/multiplexed-samples/IGVFSM3192MEUT/",
613            "accession": "IGVFSM3192MEUT",
614            "status": "preview"
615        },
616        {
617            "@id": "/multiplexed-samples/IGVFSM8298LTTJ/",
618            "accession": "IGVFSM8298LTTJ",
619            "status": "preview"
620        },
621        {
622            "@id": "/multiplexed-samples/IGVFSM0496VQZI/",
623            "accession": "IGVFSM0496VQZI",
624            "status": "preview"
625        }
626    ],
627    "origin_of": [],
628    "parts": [],
629    "pmi": 200,
630    "pmi_units": "minute",
631    "pooled_in": [],
632    "preservation_method": "flash-freezing",
633    "protocols": [
634        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
635    ],
636    "sample_terms": [
637        {
638            "@id": "/sample-terms/UBERON_0001874/",
639            "status": "preview",
640            "term_name": "putamen"
641        }
642    ],
643    "schema_version": "21",
644    "sex": "male",
645    "sorted_fractions": [],
646    "sources": [
647        {
648            "@id": "/sources/banner-health/",
649            "status": "released",
650            "title": "Banner Health"
651        }
652    ],
653    "status": "preview",
654    "submitted_by": {
655        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
656        "title": "Ryan Corces"
657    },
658    "summary": "Homo sapiens (male, 80 years) putamen tissue associated with Alzheimer disease, Parkinson's disease, cerebral amyloid angiopathy",
659    "taxa": "Homo sapiens",
660    "upper_bound_age": 80,
661    "upper_bound_age_in_hours": 700800,
662    "uuid": "6ebfcba3-d56d-4820-9d98-4c5cd4a241c1",
663    "virtual": false
664}