putamen — IGVFSM2996BWPB

preview
1{
2    "@context": "/terms/",
3    "@id": "/tissues/IGVFSM2996BWPB/",
4    "@type": [
5        "Tissue",
6        "Biosample",
7        "Sample",
8        "Item"
9    ],
10    "accession": "IGVFSM2996BWPB",
11    "age": "78",
12    "age_units": "year",
13    "aliases": [
14        "igvf:corces_tissue_BANN2103_PUT_B1"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "mismatched status",
20                "detail": "Preview tissue [IGVFSM2996BWPB](/tissues/IGVFSM2996BWPB/) 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/IGVFSM2996BWPB/"
25            },
26            {
27                "category": "missing CCF ID",
28                "detail": "Tissue [IGVFSM2996BWPB](/tissues/IGVFSM2996BWPB/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_tissue_ccf_id",
32                "path": "/tissues/IGVFSM2996BWPB/"
33            }
34        ]
35    },
36    "award": {
37        "@id": "/awards/HG012076/",
38        "component": "mapping"
39    },
40    "classifications": [
41        "tissue"
42    ],
43    "creation_timestamp": "2025-03-19T12:57:25.594539+00:00",
44    "date_obtained": "2022-10-24",
45    "disease_terms": [
46        {
47            "@id": "/phenotype-terms/DOID_14330/",
48            "status": "in progress",
49            "term_name": "Parkinson's disease"
50        }
51    ],
52    "donors": [
53        {
54            "@id": "/human-donors/IGVFDO2559GIIZ/",
55            "accession": "IGVFDO2559GIIZ",
56            "ethnicities": [
57                "European"
58            ],
59            "status": "preview"
60        }
61    ],
62    "file_sets": [
63        {
64            "@id": "/measurement-sets/IGVFDS3906MJRZ/",
65            "accession": "IGVFDS3906MJRZ",
66            "aliases": [
67                "igvf:corces_measurementSet_X010_G3_ATAC"
68            ],
69            "file_set_type": "experimental data",
70            "lab": {
71                "title": "Ryan Corces, Gladstone Institute UCSF"
72            },
73            "preferred_assay_title": "10x multiome",
74            "status": "preview",
75            "summary": "single-nucleus ATAC-seq (10x multiome)"
76        },
77        {
78            "@id": "/measurement-sets/IGVFDS3523OUSU/",
79            "accession": "IGVFDS3523OUSU",
80            "aliases": [
81                "igvf:corces_measurementSet_X010_G3_RNA"
82            ],
83            "file_set_type": "experimental data",
84            "lab": {
85                "title": "Ryan Corces, Gladstone Institute UCSF"
86            },
87            "preferred_assay_title": "10x multiome",
88            "status": "preview",
89            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
90        },
91        {
92            "@id": "/measurement-sets/IGVFDS3082IAKC/",
93            "accession": "IGVFDS3082IAKC",
94            "aliases": [
95                "igvf:corces_measurementSet_X010_G1_ATAC"
96            ],
97            "file_set_type": "experimental data",
98            "lab": {
99                "title": "Ryan Corces, Gladstone Institute UCSF"
100            },
101            "preferred_assay_title": "10x multiome",
102            "status": "preview",
103            "summary": "single-nucleus ATAC-seq (10x multiome)"
104        },
105        {
106            "@id": "/measurement-sets/IGVFDS2742JUQC/",
107            "accession": "IGVFDS2742JUQC",
108            "aliases": [
109                "igvf:corces_measurementSet_X010_G1_RNA"
110            ],
111            "file_set_type": "experimental data",
112            "lab": {
113                "title": "Ryan Corces, Gladstone Institute UCSF"
114            },
115            "preferred_assay_title": "10x multiome",
116            "status": "preview",
117            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
118        },
119        {
120            "@id": "/measurement-sets/IGVFDS2695QSNJ/",
121            "accession": "IGVFDS2695QSNJ",
122            "aliases": [
123                "igvf:corces_measurementSet_X010_G6_ATAC"
124            ],
125            "file_set_type": "experimental data",
126            "lab": {
127                "title": "Ryan Corces, Gladstone Institute UCSF"
128            },
129            "preferred_assay_title": "10x multiome",
130            "status": "preview",
131            "summary": "single-nucleus ATAC-seq (10x multiome)"
132        },
133        {
134            "@id": "/measurement-sets/IGVFDS8788ZHNN/",
135            "accession": "IGVFDS8788ZHNN",
136            "aliases": [
137                "igvf:corces_measurementSet_X010_G6_RNA"
138            ],
139            "file_set_type": "experimental data",
140            "lab": {
141                "title": "Ryan Corces, Gladstone Institute UCSF"
142            },
143            "preferred_assay_title": "10x multiome",
144            "status": "preview",
145            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
146        },
147        {
148            "@id": "/measurement-sets/IGVFDS8437JRRP/",
149            "accession": "IGVFDS8437JRRP",
150            "aliases": [
151                "igvf:corces_measurementSet_X010_G7_ATAC"
152            ],
153            "file_set_type": "experimental data",
154            "lab": {
155                "title": "Ryan Corces, Gladstone Institute UCSF"
156            },
157            "preferred_assay_title": "10x multiome",
158            "status": "preview",
159            "summary": "single-nucleus ATAC-seq (10x multiome)"
160        },
161        {
162            "@id": "/measurement-sets/IGVFDS9790PNTZ/",
163            "accession": "IGVFDS9790PNTZ",
164            "aliases": [
165                "igvf:corces_measurementSet_X010_G7_RNA"
166            ],
167            "file_set_type": "experimental data",
168            "lab": {
169                "title": "Ryan Corces, Gladstone Institute UCSF"
170            },
171            "preferred_assay_title": "10x multiome",
172            "status": "preview",
173            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
174        },
175        {
176            "@id": "/measurement-sets/IGVFDS7866JXEW/",
177            "accession": "IGVFDS7866JXEW",
178            "aliases": [
179                "igvf:corces_measurementSet_X010_G8_ATAC"
180            ],
181            "file_set_type": "experimental data",
182            "lab": {
183                "title": "Ryan Corces, Gladstone Institute UCSF"
184            },
185            "preferred_assay_title": "10x multiome",
186            "status": "preview",
187            "summary": "single-nucleus ATAC-seq (10x multiome)"
188        },
189        {
190            "@id": "/measurement-sets/IGVFDS9655EEFO/",
191            "accession": "IGVFDS9655EEFO",
192            "aliases": [
193                "igvf:corces_measurementSet_X010_G8_RNA"
194            ],
195            "file_set_type": "experimental data",
196            "lab": {
197                "title": "Ryan Corces, Gladstone Institute UCSF"
198            },
199            "preferred_assay_title": "10x multiome",
200            "status": "preview",
201            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
202        },
203        {
204            "@id": "/measurement-sets/IGVFDS5532ZXNF/",
205            "accession": "IGVFDS5532ZXNF",
206            "aliases": [
207                "igvf:corces_measurementSet_X010_G4_ATAC"
208            ],
209            "file_set_type": "experimental data",
210            "lab": {
211                "title": "Ryan Corces, Gladstone Institute UCSF"
212            },
213            "preferred_assay_title": "10x multiome",
214            "status": "preview",
215            "summary": "single-nucleus ATAC-seq (10x multiome)"
216        },
217        {
218            "@id": "/measurement-sets/IGVFDS5869YFNA/",
219            "accession": "IGVFDS5869YFNA",
220            "aliases": [
221                "igvf:corces_measurementSet_X010_G4_RNA"
222            ],
223            "file_set_type": "experimental data",
224            "lab": {
225                "title": "Ryan Corces, Gladstone Institute UCSF"
226            },
227            "preferred_assay_title": "10x multiome",
228            "status": "preview",
229            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
230        },
231        {
232            "@id": "/measurement-sets/IGVFDS2046NYYD/",
233            "accession": "IGVFDS2046NYYD",
234            "aliases": [
235                "igvf:corces_measurementSet_X010_G5_ATAC"
236            ],
237            "file_set_type": "experimental data",
238            "lab": {
239                "title": "Ryan Corces, Gladstone Institute UCSF"
240            },
241            "preferred_assay_title": "10x multiome",
242            "status": "preview",
243            "summary": "single-nucleus ATAC-seq (10x multiome)"
244        },
245        {
246            "@id": "/measurement-sets/IGVFDS6610EBRU/",
247            "accession": "IGVFDS6610EBRU",
248            "aliases": [
249                "igvf:corces_measurementSet_X010_G5_RNA"
250            ],
251            "file_set_type": "experimental data",
252            "lab": {
253                "title": "Ryan Corces, Gladstone Institute UCSF"
254            },
255            "preferred_assay_title": "10x multiome",
256            "status": "preview",
257            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
258        },
259        {
260            "@id": "/measurement-sets/IGVFDS2673QZAP/",
261            "accession": "IGVFDS2673QZAP",
262            "aliases": [
263                "igvf:corces_measurementSet_X010_G2_ATAC"
264            ],
265            "file_set_type": "experimental data",
266            "lab": {
267                "title": "Ryan Corces, Gladstone Institute UCSF"
268            },
269            "preferred_assay_title": "10x multiome",
270            "status": "preview",
271            "summary": "single-nucleus ATAC-seq (10x multiome)"
272        },
273        {
274            "@id": "/measurement-sets/IGVFDS6589NGAU/",
275            "accession": "IGVFDS6589NGAU",
276            "aliases": [
277                "igvf:corces_measurementSet_X010_G2_RNA"
278            ],
279            "file_set_type": "experimental data",
280            "lab": {
281                "title": "Ryan Corces, Gladstone Institute UCSF"
282            },
283            "preferred_assay_title": "10x multiome",
284            "status": "preview",
285            "summary": "single-nucleus RNA sequencing assay (10x multiome)"
286        }
287    ],
288    "institutional_certificates": [
289        {
290            "@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
291            "certificate_identifier": "IP115-05",
292            "controlled_access": false,
293            "status": "in progress"
294        }
295    ],
296    "lab": {
297        "@id": "/labs/ryan-corces/",
298        "title": "Ryan Corces, Gladstone Institute UCSF"
299    },
300    "lower_bound_age": 78,
301    "lower_bound_age_in_hours": 683280,
302    "multiplexed_in": [
303        {
304            "@id": "/multiplexed-samples/IGVFSM7630MDYJ/",
305            "accession": "IGVFSM7630MDYJ",
306            "status": "preview"
307        },
308        {
309            "@id": "/multiplexed-samples/IGVFSM2403GODW/",
310            "accession": "IGVFSM2403GODW",
311            "status": "preview"
312        },
313        {
314            "@id": "/multiplexed-samples/IGVFSM3084IVUH/",
315            "accession": "IGVFSM3084IVUH",
316            "status": "preview"
317        },
318        {
319            "@id": "/multiplexed-samples/IGVFSM6456NQTK/",
320            "accession": "IGVFSM6456NQTK",
321            "status": "preview"
322        },
323        {
324            "@id": "/multiplexed-samples/IGVFSM4584XRDP/",
325            "accession": "IGVFSM4584XRDP",
326            "status": "preview"
327        },
328        {
329            "@id": "/multiplexed-samples/IGVFSM9228FDFE/",
330            "accession": "IGVFSM9228FDFE",
331            "status": "preview"
332        },
333        {
334            "@id": "/multiplexed-samples/IGVFSM9348OQXF/",
335            "accession": "IGVFSM9348OQXF",
336            "status": "preview"
337        },
338        {
339            "@id": "/multiplexed-samples/IGVFSM3089OHDA/",
340            "accession": "IGVFSM3089OHDA",
341            "status": "preview"
342        }
343    ],
344    "origin_of": [],
345    "part_of": "/tissues/IGVFSM8221WAEF/",
346    "parts": [],
347    "pmi": 250,
348    "pmi_units": "minute",
349    "pooled_in": [],
350    "preservation_method": "flash-freezing",
351    "protocols": [
352        "https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-snmulti-6uchesw"
353    ],
354    "sample_terms": [
355        {
356            "@id": "/sample-terms/UBERON_0001874/",
357            "status": "preview",
358            "term_name": "putamen"
359        }
360    ],
361    "schema_version": "21",
362    "sex": "male",
363    "sorted_fractions": [],
364    "sources": [
365        {
366            "@id": "/sources/banner-health/",
367            "status": "released",
368            "title": "Banner Health"
369        }
370    ],
371    "status": "preview",
372    "submitted_by": {
373        "@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
374        "title": "Ryan Corces"
375    },
376    "summary": "Homo sapiens (male, 78 years) putamen tissue associated with Parkinson's disease",
377    "taxa": "Homo sapiens",
378    "upper_bound_age": 78,
379    "upper_bound_age_in_hours": 683280,
380    "uuid": "33527250-f8be-4884-bead-3fc6dd04cc62",
381    "virtual": false
382}