IGVFDS7388FOPN

1{
2    "@context": "/terms/",
3    "@id": "/analysis-sets/IGVFDS7388FOPN/",
4    "@type": [
5        "AnalysisSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS7388FOPN",
10    "aliases": [
11        "ansuman-satpathy:igvf16_analysis_set",
12        "ansuman-satpathy:igvf16_analysis_set_10x1"
13    ],
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "audit": {
18        "INTERNAL_ACTION": [
19            {
20                "category": "mismatched status",
21                "detail": "Released multiplexed sample [IGVFSM3549KFGD](/multiplexed-samples/IGVFSM3549KFGD/) has in progress subobject tabular file [IGVFFI2383CFVI](/tabular-files/IGVFFI2383CFVI/).",
22                "level": 30,
23                "level_name": "INTERNAL_ACTION",
24                "name": "audit_item_status",
25                "path": "/multiplexed-samples/IGVFSM3549KFGD/"
26            },
27            {
28                "category": "mismatched status",
29                "detail": "Released matrix file [IGVFFI6583WSWL](/matrix-files/IGVFFI6583WSWL/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
30                "level": 30,
31                "level_name": "INTERNAL_ACTION",
32                "name": "audit_item_status",
33                "path": "/matrix-files/IGVFFI6583WSWL/"
34            },
35            {
36                "category": "mismatched status",
37                "detail": "Released matrix file [IGVFFI6583WSWL](/matrix-files/IGVFFI6583WSWL/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
38                "level": 30,
39                "level_name": "INTERNAL_ACTION",
40                "name": "audit_item_status",
41                "path": "/matrix-files/IGVFFI6583WSWL/"
42            },
43            {
44                "category": "missing demultiplexed sample",
45                "detail": "Analysis set [IGVFDS7388FOPN](/analysis-sets/IGVFDS7388FOPN/) has `input_file_sets` with multiplexed samples: [IGVFSM3549KFGD](/multiplexed-samples/IGVFSM3549KFGD/) but no `demultiplexed_sample`. Analysis sets with multiplexed samples are expected to specify a demultiplexed sample.",
46                "level": 30,
47                "level_name": "INTERNAL_ACTION",
48                "name": "audit_analysis_set_multiplexed_samples",
49                "path": "/analysis-sets/IGVFDS7388FOPN/"
50            }
51        ]
52    },
53    "award": {
54        "@id": "/awards/HG012076/",
55        "component": "mapping",
56        "contact_pi": {
57            "@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
58            "title": "Ansuman Satpathy"
59        },
60        "title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
61    },
62    "control_for": [],
63    "controlled_access": true,
64    "creation_timestamp": "2025-02-14T21:32:47.904327+00:00",
65    "data_use_limitation_summaries": [
66        "GRU"
67    ],
68    "description": "Quality-control workflow performed by Satpathy Lab - iPSC village pancreatic differentiation",
69    "donors": [
70        {
71            "@id": "/human-donors/IGVFDO0657EMJH/",
72            "accession": "IGVFDO0657EMJH",
73            "aliases": [
74                "ansuman-satpathy:donor_of_GM01652",
75                "igvf:donor_GM01652"
76            ],
77            "sex": "female",
78            "status": "released",
79            "taxa": "Homo sapiens"
80        },
81        {
82            "@id": "/human-donors/IGVFDO5614PTYQ/",
83            "accession": "IGVFDO5614PTYQ",
84            "aliases": [
85                "ansuman-satpathy:donor_of_A004",
86                "igvf:donor_A004"
87            ],
88            "sex": "male",
89            "status": "released",
90            "taxa": "Homo sapiens"
91        },
92        {
93            "@id": "/human-donors/IGVFDO4452ZQSF/",
94            "accession": "IGVFDO4452ZQSF",
95            "aliases": [
96                "ansuman-satpathy:donor_of_B010",
97                "igvf:donor_B010"
98            ],
99            "sex": "male",
100            "status": "released",
101            "taxa": "Homo sapiens"
102        },
103        {
104            "@id": "/human-donors/IGVFDO6638HIAD/",
105            "accession": "IGVFDO6638HIAD",
106            "aliases": [
107                "igvf:donor_of_H1"
108            ],
109            "sex": "male",
110            "status": "released",
111            "taxa": "Homo sapiens"
112        },
113        {
114            "@id": "/human-donors/IGVFDO4134ZWBU/",
115            "accession": "IGVFDO4134ZWBU",
116            "aliases": [
117                "ansuman-satpathy:donor_of_B005",
118                "igvf:donor_B005"
119            ],
120            "sex": "male",
121            "status": "released",
122            "taxa": "Homo sapiens"
123        },
124        {
125            "@id": "/human-donors/IGVFDO9617JBWJ/",
126            "accession": "IGVFDO9617JBWJ",
127            "aliases": [
128                "ansuman-satpathy:donor_of_B002",
129                "igvf:donor_B002"
130            ],
131            "sex": "female",
132            "status": "released",
133            "taxa": "Homo sapiens"
134        },
135        {
136            "@id": "/human-donors/IGVFDO1364EAZP/",
137            "accession": "IGVFDO1364EAZP",
138            "aliases": [
139                "ansuman-satpathy:donor_of_PENN086i-278-1",
140                "igvf:donor_PENN086i-278-1"
141            ],
142            "sex": "male",
143            "status": "released",
144            "taxa": "Homo sapiens"
145        },
146        {
147            "@id": "/human-donors/IGVFDO7650ICPB/",
148            "accession": "IGVFDO7650ICPB",
149            "aliases": [
150                "ansuman-satpathy:donor_of_B001",
151                "igvf:donor_B001"
152            ],
153            "sex": "male",
154            "status": "released",
155            "taxa": "Homo sapiens"
156        },
157        {
158            "@id": "/human-donors/IGVFDO0183MFIP/",
159            "accession": "IGVFDO0183MFIP",
160            "aliases": [
161                "ansuman-satpathy:donor_of_KOLF2.2J",
162                "igvf:donor_KOLF2.2J"
163            ],
164            "sex": "male",
165            "status": "released",
166            "taxa": "Homo sapiens"
167        },
168        {
169            "@id": "/human-donors/IGVFDO8129FWUV/",
170            "accession": "IGVFDO8129FWUV",
171            "aliases": [
172                "ansuman-satpathy:donor_of_B011",
173                "igvf:donor_B011"
174            ],
175            "sex": "female",
176            "status": "released",
177            "taxa": "Homo sapiens"
178        },
179        {
180            "@id": "/human-donors/IGVFDO8977PNMK/",
181            "accession": "IGVFDO8977PNMK",
182            "aliases": [
183                "ansuman-satpathy:donor_of_C001",
184                "igvf:donor_C001"
185            ],
186            "sex": "female",
187            "status": "released",
188            "taxa": "Homo sapiens"
189        },
190        {
191            "@id": "/human-donors/IGVFDO6162MIWK/",
192            "accession": "IGVFDO6162MIWK",
193            "aliases": [
194                "ansuman-satpathy:donor_of_WA26",
195                "igvf:donor_WA26"
196            ],
197            "sex": "female",
198            "status": "released",
199            "taxa": "Homo sapiens"
200        },
201        {
202            "@id": "/human-donors/IGVFDO2817PSCX/",
203            "accession": "IGVFDO2817PSCX",
204            "aliases": [
205                "ansuman-satpathy:donor_of_A009",
206                "igvf:donor_A009"
207            ],
208            "sex": "female",
209            "status": "released",
210            "taxa": "Homo sapiens"
211        },
212        {
213            "@id": "/human-donors/IGVFDO2620HPCX/",
214            "accession": "IGVFDO2620HPCX",
215            "aliases": [
216                "ansuman-satpathy:donor_of_B003",
217                "igvf:donor_B003"
218            ],
219            "sex": "female",
220            "status": "released",
221            "taxa": "Homo sapiens"
222        },
223        {
224            "@id": "/human-donors/IGVFDO2379DTAU/",
225            "accession": "IGVFDO2379DTAU",
226            "aliases": [
227                "ansuman-satpathy:donor_of_A007",
228                "igvf:donor_A007"
229            ],
230            "sex": "female",
231            "status": "released",
232            "taxa": "Homo sapiens"
233        },
234        {
235            "@id": "/human-donors/IGVFDO8129UUAA/",
236            "accession": "IGVFDO8129UUAA",
237            "aliases": [
238                "ansuman-satpathy:donor_of_C008",
239                "igvf:donor_C008"
240            ],
241            "sex": "female",
242            "status": "released",
243            "taxa": "Homo sapiens"
244        },
245        {
246            "@id": "/human-donors/IGVFDO2650AGWB/",
247            "accession": "IGVFDO2650AGWB",
248            "aliases": [
249                "ansuman-satpathy:donor_of_WA14",
250                "igvf:donor_WA14"
251            ],
252            "sex": "male",
253            "status": "released",
254            "taxa": "Homo sapiens"
255        },
256        {
257            "@id": "/human-donors/IGVFDO5729MXSO/",
258            "accession": "IGVFDO5729MXSO",
259            "aliases": [
260                "ansuman-satpathy:donor_of_B008",
261                "igvf:donor_B008"
262            ],
263            "sex": "female",
264            "status": "released",
265            "taxa": "Homo sapiens"
266        },
267        {
268            "@id": "/human-donors/IGVFDO6441FSJH/",
269            "accession": "IGVFDO6441FSJH",
270            "aliases": [
271                "ansuman-satpathy:donor_of_A003",
272                "igvf:donor_A003"
273            ],
274            "sex": "female",
275            "status": "released",
276            "taxa": "Homo sapiens"
277        },
278        {
279            "@id": "/human-donors/IGVFDO7470LCGC/",
280            "accession": "IGVFDO7470LCGC",
281            "aliases": [
282                "ansuman-satpathy:donor_of_WA25",
283                "igvf:donor_WA25"
284            ],
285            "sex": "female",
286            "status": "released",
287            "taxa": "Homo sapiens"
288        },
289        {
290            "@id": "/human-donors/IGVFDO4876ENMD/",
291            "accession": "IGVFDO4876ENMD",
292            "aliases": [
293                "ansuman-satpathy:donor_of_C007",
294                "igvf:donor_C007"
295            ],
296            "sex": "female",
297            "status": "released",
298            "taxa": "Homo sapiens"
299        },
300        {
301            "@id": "/human-donors/IGVFDO2718IDDQ/",
302            "accession": "IGVFDO2718IDDQ",
303            "aliases": [
304                "igvf:donor_of_H9"
305            ],
306            "sex": "female",
307            "status": "released",
308            "taxa": "Homo sapiens"
309        },
310        {
311            "@id": "/human-donors/IGVFDO0324ZSAY/",
312            "accession": "IGVFDO0324ZSAY",
313            "aliases": [
314                "ansuman-satpathy:donor_of_PENN020i-588-6",
315                "igvf:donor_PENN0201-588-6"
316            ],
317            "sex": "female",
318            "status": "released",
319            "taxa": "Homo sapiens"
320        },
321        {
322            "@id": "/human-donors/IGVFDO5656YCPC/",
323            "accession": "IGVFDO5656YCPC",
324            "aliases": [
325                "ansuman-satpathy:donor_of_Mel-1",
326                "igvf:donor_Mel-1"
327            ],
328            "sex": "male",
329            "status": "released",
330            "taxa": "Homo sapiens"
331        },
332        {
333            "@id": "/human-donors/IGVFDO0720ONIQ/",
334            "accession": "IGVFDO0720ONIQ",
335            "aliases": [
336                "ansuman-satpathy:donor_of_C004",
337                "igvf:donor_C004"
338            ],
339            "sex": "female",
340            "status": "released",
341            "taxa": "Homo sapiens"
342        },
343        {
344            "@id": "/human-donors/IGVFDO6169GISQ/",
345            "accession": "IGVFDO6169GISQ",
346            "aliases": [
347                "ansuman-satpathy:donor_of_B009",
348                "igvf:donor_B009"
349            ],
350            "sex": "male",
351            "status": "released",
352            "taxa": "Homo sapiens"
353        },
354        {
355            "@id": "/human-donors/IGVFDO4001VEAC/",
356            "accession": "IGVFDO4001VEAC",
357            "aliases": [
358                "ansuman-satpathy:donor_of_XM001",
359                "igvf:donor_XM001"
360            ],
361            "sex": "female",
362            "status": "released",
363            "taxa": "Homo sapiens"
364        },
365        {
366            "@id": "/human-donors/IGVFDO8893DMFF/",
367            "accession": "IGVFDO8893DMFF",
368            "aliases": [
369                "ansuman-satpathy:donor_of_B006",
370                "igvf:donor_B006"
371            ],
372            "sex": "male",
373            "status": "released",
374            "taxa": "Homo sapiens"
375        },
376        {
377            "@id": "/human-donors/IGVFDO9716HDYX/",
378            "accession": "IGVFDO9716HDYX",
379            "aliases": [
380                "ansuman-satpathy:donor_of_A002",
381                "igvf:donor_A002"
382            ],
383            "sex": "male",
384            "status": "released",
385            "taxa": "Homo sapiens"
386        },
387        {
388            "@id": "/human-donors/IGVFDO7670TOWV/",
389            "accession": "IGVFDO7670TOWV",
390            "aliases": [
391                "ansuman-satpathy:donor_of_B012",
392                "igvf:donor_B012"
393            ],
394            "sex": "female",
395            "status": "released",
396            "taxa": "Homo sapiens"
397        },
398        {
399            "@id": "/human-donors/IGVFDO8315PGTI/",
400            "accession": "IGVFDO8315PGTI",
401            "aliases": [
402                "igvf:donor_HUES8"
403            ],
404            "sex": "male",
405            "status": "released",
406            "taxa": "Homo sapiens"
407        },
408        {
409            "@id": "/human-donors/IGVFDO4532PFAJ/",
410            "accession": "IGVFDO4532PFAJ",
411            "aliases": [
412                "ansuman-satpathy:donor_of_A010",
413                "igvf:donor_A010"
414            ],
415            "sex": "female",
416            "status": "released",
417            "taxa": "Homo sapiens"
418        },
419        {
420            "@id": "/human-donors/IGVFDO7725MEWB/",
421            "accession": "IGVFDO7725MEWB",
422            "aliases": [
423                "ansuman-satpathy:donor_of_GM00731",
424                "igvf:donor_GM00731"
425            ],
426            "sex": "male",
427            "status": "released",
428            "taxa": "Homo sapiens"
429        },
430        {
431            "@id": "/human-donors/IGVFDO1038DAII/",
432            "accession": "IGVFDO1038DAII",
433            "aliases": [
434                "ansuman-satpathy:donor_of_Hues6",
435                "igvf:donor_Hues6"
436            ],
437            "sex": "female",
438            "status": "released",
439            "taxa": "Homo sapiens"
440        },
441        {
442            "@id": "/human-donors/IGVFDO1221XJAX/",
443            "accession": "IGVFDO1221XJAX",
444            "aliases": [
445                "ansuman-satpathy:donor_of_WA13",
446                "igvf:donor_WA13"
447            ],
448            "sex": "male",
449            "status": "released",
450            "taxa": "Homo sapiens"
451        },
452        {
453            "@id": "/human-donors/IGVFDO7140TLQJ/",
454            "accession": "IGVFDO7140TLQJ",
455            "aliases": [
456                "ansuman-satpathy:donor_of_Hues9",
457                "igvf:donor_Hues9"
458            ],
459            "sex": "female",
460            "status": "released",
461            "taxa": "Homo sapiens"
462        },
463        {
464            "@id": "/human-donors/IGVFDO2492CCQG/",
465            "accession": "IGVFDO2492CCQG",
466            "aliases": [
467                "ansuman-satpathy:donor_of_B004",
468                "igvf:donor_B004"
469            ],
470            "sex": "female",
471            "status": "released",
472            "taxa": "Homo sapiens"
473        },
474        {
475            "@id": "/human-donors/IGVFDO9904ZSML/",
476            "accession": "IGVFDO9904ZSML",
477            "aliases": [
478                "ansuman-satpathy:donor_of_RUES1",
479                "igvf:donor_RUES1"
480            ],
481            "sex": "male",
482            "status": "released",
483            "taxa": "Homo sapiens"
484        },
485        {
486            "@id": "/human-donors/IGVFDO2965ZTUG/",
487            "accession": "IGVFDO2965ZTUG",
488            "aliases": [
489                "ansuman-satpathy:donor_of_GM01680",
490                "igvf:donor_GM01680"
491            ],
492            "sex": "female",
493            "status": "released",
494            "taxa": "Homo sapiens"
495        },
496        {
497            "@id": "/human-donors/IGVFDO3755LIBB/",
498            "accession": "IGVFDO3755LIBB",
499            "aliases": [
500                "ansuman-satpathy:donor_of_A006",
501                "igvf:donor_A006"
502            ],
503            "sex": "male",
504            "status": "released",
505            "taxa": "Homo sapiens"
506        },
507        {
508            "@id": "/human-donors/IGVFDO7813GMND/",
509            "accession": "IGVFDO7813GMND",
510            "aliases": [
511                "ansuman-satpathy:donor_of_A001",
512                "igvf:donor_A001"
513            ],
514            "sex": "female",
515            "status": "released",
516            "taxa": "Homo sapiens"
517        },
518        {
519            "@id": "/human-donors/IGVFDO1964RNHE/",
520            "accession": "IGVFDO1964RNHE",
521            "aliases": [
522                "ansuman-satpathy:donor_of_C003",
523                "igvf:donor_C003"
524            ],
525            "sex": "male",
526            "status": "released",
527            "taxa": "Homo sapiens"
528        },
529        {
530            "@id": "/human-donors/IGVFDO5261UCLF/",
531            "accession": "IGVFDO5261UCLF",
532            "aliases": [
533                "igvf:donor_of_RUES2",
534                "igvf:donor_RUES2"
535            ],
536            "sex": "female",
537            "status": "released",
538            "taxa": "Homo sapiens"
539        },
540        {
541            "@id": "/human-donors/IGVFDO2750DZPB/",
542            "accession": "IGVFDO2750DZPB",
543            "aliases": [
544                "ansuman-satpathy:donor_of_B007",
545                "igvf:donor_B007"
546            ],
547            "sex": "male",
548            "status": "released",
549            "taxa": "Homo sapiens"
550        }
551    ],
552    "file_set_type": "intermediate analysis",
553    "files": [
554        {
555            "@id": "/tabular-files/IGVFFI4068UGBT/",
556            "accession": "IGVFFI4068UGBT",
557            "aliases": [
558                "ansuman-satpathy:igvf16_fragments_10x1"
559            ],
560            "content_type": "fragments",
561            "controlled_access": true,
562            "creation_timestamp": "2025-02-14T22:50:41.838247+00:00",
563            "file_format": "tsv",
564            "file_size": 5134192255,
565            "href": "/tabular-files/IGVFFI4068UGBT/@@download/IGVFFI4068UGBT.tsv.gz",
566            "s3_uri": "s3://igvf-restricted-files/2025/02/14/496777ed-9a93-4706-aa7e-1b3677c608d7/IGVFFI4068UGBT.tsv.gz",
567            "status": "released",
568            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l1_fragments.tsv.gz",
569            "upload_status": "validation exempted"
570        },
571        {
572            "@id": "/tabular-files/IGVFFI7838CPRY/",
573            "accession": "IGVFFI7838CPRY",
574            "aliases": [
575                "ansuman-satpathy:igvf16_peaks_10x1"
576            ],
577            "assembly": "GRCh38",
578            "content_type": "peaks",
579            "controlled_access": true,
580            "creation_timestamp": "2025-02-14T22:51:09.989625+00:00",
581            "file_format": "bed",
582            "file_size": 2789314,
583            "href": "/tabular-files/IGVFFI7838CPRY/@@download/IGVFFI7838CPRY.bed.gz",
584            "s3_uri": "s3://igvf-restricted-files/2025/02/14/81e78d74-017f-4607-adb8-31b687b5c5a0/IGVFFI7838CPRY.bed.gz",
585            "status": "released",
586            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l1_peaks.bed.gz",
587            "upload_status": "validation exempted"
588        },
589        {
590            "@id": "/index-files/IGVFFI4057QTFY/",
591            "accession": "IGVFFI4057QTFY",
592            "aliases": [
593                "ansuman-satpathy:igvf16_fragments_index_10x1"
594            ],
595            "content_type": "index",
596            "controlled_access": true,
597            "creation_timestamp": "2025-02-14T23:07:27.042329+00:00",
598            "file_format": "tbi",
599            "file_size": 1698138,
600            "href": "/index-files/IGVFFI4057QTFY/@@download/IGVFFI4057QTFY.tbi",
601            "s3_uri": "s3://igvf-restricted-files/2025/02/14/a89e451f-4af1-478b-8e22-e9686ee4e613/IGVFFI4057QTFY.tbi",
602            "status": "released",
603            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf16/e16l1_fragments.tsv.gz.tbi",
604            "upload_status": "validated"
605        },
606        {
607            "@id": "/matrix-files/IGVFFI6583WSWL/",
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609            "aliases": [
610                "ansuman-satpathy:igvf16_raw_rna_counts_10x1"
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620            "upload_status": "validated"
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624            "accession": "IGVFFI9758JFVL",
625            "aliases": [
626                "ansuman-satpathy:igvf16_multiseq_count_matrix_10x1"
627            ],
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630            "creation_timestamp": "2025-02-19T23:37:44.400141+00:00",
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636            "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/multi_tsvs/e16l1_tag_mtx.tsv.gz",
637            "upload_status": "validated"
638        }
639    ],
640    "functional_assay_mechanisms": [],
641    "input_file_sets": [
642        {
643            "@id": "/measurement-sets/IGVFDS7129TVLQ/",
644            "accession": "IGVFDS7129TVLQ",
645            "aliases": [
646                "ansuman-satpathy:snRNA-seq_igvf16_10x1"
647            ],
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654            "aliases": [
655                "ansuman-satpathy:multiseq_igvf16_10x1"
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664                "ansuman-satpathy:snATAC-seq_igvf16_10x1"
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671    "lab": {
672        "@id": "/labs/ansuman-satpathy/",
673        "title": "Ansuman Satpathy, Stanford"
674    },
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676        "https://www.protocols.io/view/multi-seq-for-multiome-igvf-round-2-experiment-1-dfqp3mvn"
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678    "release_timestamp": "2025-03-22T00:42:04.657044+00:00",
679    "sample_summary": "Homo sapiens multiplexed sample of induced pluripotent stem cell",
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681        {
682            "@id": "/multiplexed-samples/IGVFSM3549KFGD/",
683            "@type": [
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689            "aliases": [
690                "ansuman-satpathy:multiplexed_sample_igvf16_10x1"
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692            "cellular_sub_pool": "1",
693            "classifications": [
694                "differentiated cell specimen",
695                "multiplexed sample"
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697            "disease_terms": [],
698            "institutional_certificates": [
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700                    "@id": "/institutional-certificates/1926d993-629d-42d9-a962-f391ea6ee18f/",
701                    "certificate_identifier": "IP115-23",
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703                    "data_use_limitation": "GRU",
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707            "modifications": [],
708            "sample_terms": [
709                {
710                    "@id": "/sample-terms/EFO_0004905/",
711                    "@type": [
712                        "SampleTerm",
713                        "OntologyTerm",
714                        "Item"
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721            "status": "released",
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723            "taxa": "Homo sapiens",
724            "treatments": []
725        }
726    ],
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728    "status": "released",
729    "submitted_by": {
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731        "title": "Christopher Mcginnis"
732    },
733    "submitted_files_timestamp": "2025-02-14T22:50:41.838247+00:00",
734    "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix",
735    "uuid": "80773495-97c2-43da-9385-e2a77642b0f2",
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739            "accession": "IGVFWF1453HVEC",
740            "name": "Satpathy Cell Ranger",
741            "status": "released",
742            "uniform_pipeline": false
743        }
744    ]
745}