IGVFDS7938OXSK

1{
2    "@context": "/terms/",
3    "@id": "/measurement-sets/IGVFDS7938OXSK/",
4    "@type": [
5        "MeasurementSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS7938OXSK",
10    "aliases": [
11        "buenrostro-bernstein:scRNA Lib 609"
12    ],
13    "assay_term": {
14        "@id": "/assay-terms/OBI_0002631/",
15        "assay_slims": [
16            "gene expression"
17        ],
18        "status": "released",
19        "term_name": "single-cell RNA sequencing assay"
20    },
21    "audit": {
22        "INTERNAL_ACTION": [
23            {
24                "category": "missing publication",
25                "detail": "Tissue [IGVFSM2881UHTO](/tissues/IGVFSM2881UHTO/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
26                "level": 30,
27                "level_name": "INTERNAL_ACTION",
28                "name": "audit_sample_missing_publication",
29                "path": "/tissues/IGVFSM2881UHTO/"
30            },
31            {
32                "category": "missing publication",
33                "detail": "Measurement set [IGVFDS7938OXSK](/measurement-sets/IGVFDS7938OXSK/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
34                "level": 30,
35                "level_name": "INTERNAL_ACTION",
36                "name": "audit_file_set_missing_publication",
37                "path": "/measurement-sets/IGVFDS7938OXSK/"
38            },
39            {
40                "category": "mismatched status",
41                "detail": "Released measurement set [IGVFDS7938OXSK](/measurement-sets/IGVFDS7938OXSK/) has in progress subobject tabular file [IGVFFI9034HUWG](/tabular-files/IGVFFI9034HUWG/).",
42                "level": 30,
43                "level_name": "INTERNAL_ACTION",
44                "name": "audit_item_status",
45                "path": "/measurement-sets/IGVFDS7938OXSK/"
46            },
47            {
48                "category": "mismatched status",
49                "detail": "Released measurement set [IGVFDS7938OXSK](/measurement-sets/IGVFDS7938OXSK/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
50                "level": 30,
51                "level_name": "INTERNAL_ACTION",
52                "name": "audit_item_status",
53                "path": "/measurement-sets/IGVFDS7938OXSK/"
54            }
55        ],
56        "NOT_COMPLIANT": [
57            {
58                "category": "missing strand specificity",
59                "detail": "Measurement set [IGVFDS7938OXSK](/measurement-sets/IGVFDS7938OXSK/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
60                "level": 50,
61                "level_name": "NOT_COMPLIANT",
62                "name": "audit_missing_strand_specificity",
63                "path": "/measurement-sets/IGVFDS7938OXSK/"
64            }
65        ],
66        "WARNING": [
67            {
68                "category": "missing age",
69                "detail": "Tissue [IGVFSM2881UHTO](/tissues/IGVFSM2881UHTO/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
70                "level": 40,
71                "level_name": "WARNING",
72                "name": "audit_biosample_age",
73                "path": "/tissues/IGVFSM2881UHTO/"
74            }
75        ]
76    },
77    "award": {
78        "@id": "/awards/HG011986/",
79        "component": "mapping",
80        "contact_pi": {
81            "@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
82            "title": "Jason Buenrostro"
83        },
84        "title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
85    },
86    "control_for": [],
87    "creation_timestamp": "2025-03-09T15:52:00.612797+00:00",
88    "donors": [
89        {
90            "@id": "/rodent-donors/IGVFDO9446AKYF/",
91            "accession": "IGVFDO9446AKYF",
92            "aliases": [
93                "buenrostro-bernstein:Donor 2047"
94            ],
95            "sex": "unspecified",
96            "status": "released",
97            "taxa": "Mus musculus"
98        }
99    ],
100    "externally_hosted": false,
101    "file_set_type": "experimental data",
102    "files": [
103        {
104            "@id": "/sequence-files/IGVFFI1620FHAB/",
105            "accession": "IGVFFI1620FHAB",
106            "aliases": [
107                "buenrostro-bernstein:SS-LS_7380_R1"
108            ],
109            "content_type": "reads",
110            "controlled_access": false,
111            "creation_timestamp": "2025-03-09T15:58:51.233721+00:00",
112            "file_format": "fastq",
113            "file_size": 7975326779,
114            "href": "/sequence-files/IGVFFI1620FHAB/@@download/IGVFFI1620FHAB.fastq.gz",
115            "s3_uri": "s3://igvf-files/2025/03/09/312c8b4f-6935-4232-bff5-3b0e74d7ec71/IGVFFI1620FHAB.fastq.gz",
116            "sequencing_platform": {
117                "@id": "/platform-terms/EFO_0008637/",
118                "status": "released",
119                "term_name": "Illumina NovaSeq 6000"
120            },
121            "status": "released",
122            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1916_L8_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
123            "upload_status": "validated"
124        },
125        {
126            "@id": "/sequence-files/IGVFFI9110GXHY/",
127            "accession": "IGVFFI9110GXHY",
128            "aliases": [
129                "buenrostro-bernstein:SS-LS_7380_R2"
130            ],
131            "content_type": "reads",
132            "controlled_access": false,
133            "creation_timestamp": "2025-03-09T15:58:52.793831+00:00",
134            "file_format": "fastq",
135            "file_size": 13867924026,
136            "href": "/sequence-files/IGVFFI9110GXHY/@@download/IGVFFI9110GXHY.fastq.gz",
137            "s3_uri": "s3://igvf-files/2025/03/09/9562bd2c-7850-46c1-b8ad-0d26bcc87589/IGVFFI9110GXHY.fastq.gz",
138            "sequencing_platform": {
139                "@id": "/platform-terms/EFO_0008637/",
140                "status": "released",
141                "term_name": "Illumina NovaSeq 6000"
142            },
143            "status": "released",
144            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1916_L8_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
145            "upload_status": "validated"
146        },
147        {
148            "@id": "/sequence-files/IGVFFI7735CDGU/",
149            "accession": "IGVFFI7735CDGU",
150            "aliases": [
151                "buenrostro-bernstein:SS-LS_5381_R1"
152            ],
153            "content_type": "reads",
154            "controlled_access": false,
155            "creation_timestamp": "2025-03-09T15:59:42.278103+00:00",
156            "file_format": "fastq",
157            "file_size": 4050591869,
158            "href": "/sequence-files/IGVFFI7735CDGU/@@download/IGVFFI7735CDGU.fastq.gz",
159            "s3_uri": "s3://igvf-files/2025/03/09/e1825735-b5ec-471b-97df-418a96f215af/IGVFFI7735CDGU.fastq.gz",
160            "sequencing_platform": {
161                "@id": "/platform-terms/EFO_0008637/",
162                "status": "released",
163                "term_name": "Illumina NovaSeq 6000"
164            },
165            "status": "released",
166            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1590_L5_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
167            "upload_status": "validated"
168        },
169        {
170            "@id": "/sequence-files/IGVFFI3521DARM/",
171            "accession": "IGVFFI3521DARM",
172            "aliases": [
173                "buenrostro-bernstein:SS-LS_5381_R2"
174            ],
175            "content_type": "reads",
176            "controlled_access": false,
177            "creation_timestamp": "2025-03-09T15:59:43.537186+00:00",
178            "file_format": "fastq",
179            "file_size": 6881658359,
180            "href": "/sequence-files/IGVFFI3521DARM/@@download/IGVFFI3521DARM.fastq.gz",
181            "s3_uri": "s3://igvf-files/2025/03/09/4c420b0d-7058-4d68-a790-44a1c697fb8d/IGVFFI3521DARM.fastq.gz",
182            "sequencing_platform": {
183                "@id": "/platform-terms/EFO_0008637/",
184                "status": "released",
185                "term_name": "Illumina NovaSeq 6000"
186            },
187            "status": "released",
188            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1590_L5_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
189            "upload_status": "validated"
190        },
191        {
192            "@id": "/sequence-files/IGVFFI5362KWQZ/",
193            "accession": "IGVFFI5362KWQZ",
194            "aliases": [
195                "buenrostro-bernstein:SS-LS_5376_R1"
196            ],
197            "content_type": "reads",
198            "controlled_access": false,
199            "creation_timestamp": "2025-03-09T15:59:56.939221+00:00",
200            "file_format": "fastq",
201            "file_size": 3850010990,
202            "href": "/sequence-files/IGVFFI5362KWQZ/@@download/IGVFFI5362KWQZ.fastq.gz",
203            "s3_uri": "s3://igvf-files/2025/03/09/d065940b-3d2c-430d-aae5-ff4630435950/IGVFFI5362KWQZ.fastq.gz",
204            "sequencing_platform": {
205                "@id": "/platform-terms/EFO_0008637/",
206                "status": "released",
207                "term_name": "Illumina NovaSeq 6000"
208            },
209            "status": "released",
210            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1590_L4_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
211            "upload_status": "validated"
212        },
213        {
214            "@id": "/sequence-files/IGVFFI6526BCJI/",
215            "accession": "IGVFFI6526BCJI",
216            "aliases": [
217                "buenrostro-bernstein:SS-LS_5376_R2"
218            ],
219            "content_type": "reads",
220            "controlled_access": false,
221            "creation_timestamp": "2025-03-09T15:59:58.164326+00:00",
222            "file_format": "fastq",
223            "file_size": 6497135622,
224            "href": "/sequence-files/IGVFFI6526BCJI/@@download/IGVFFI6526BCJI.fastq.gz",
225            "s3_uri": "s3://igvf-files/2025/03/09/ad87ff42-4405-4f9e-89c4-f7da960aacbd/IGVFFI6526BCJI.fastq.gz",
226            "sequencing_platform": {
227                "@id": "/platform-terms/EFO_0008637/",
228                "status": "released",
229                "term_name": "Illumina NovaSeq 6000"
230            },
231            "status": "released",
232            "submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1590_L4_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
233            "upload_status": "validated"
234        },
235        {
236            "@id": "/configuration-files/IGVFFI0432LITC/",
237            "accession": "IGVFFI0432LITC",
238            "aliases": [
239                "buenrostro-bernstein:SS-LS_7380_seqspec"
240            ],
241            "content_type": "seqspec",
242            "creation_timestamp": "2025-03-13T17:53:57.105761+00:00",
243            "file_format": "yaml",
244            "file_size": 1289,
245            "href": "/configuration-files/IGVFFI0432LITC/@@download/IGVFFI0432LITC.yaml.gz",
246            "s3_uri": "s3://igvf-files/2025/03/13/bad356b9-b84e-499e-82b9-93362b39d376/IGVFFI0432LITC.yaml.gz",
247            "status": "released",
248            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_7380_seqspec.yaml.gz",
249            "upload_status": "validated"
250        },
251        {
252            "@id": "/configuration-files/IGVFFI2897TNFT/",
253            "accession": "IGVFFI2897TNFT",
254            "aliases": [
255                "buenrostro-bernstein:SS-LS_5381_seqspec"
256            ],
257            "content_type": "seqspec",
258            "creation_timestamp": "2025-03-13T17:54:08.673494+00:00",
259            "file_format": "yaml",
260            "file_size": 1286,
261            "href": "/configuration-files/IGVFFI2897TNFT/@@download/IGVFFI2897TNFT.yaml.gz",
262            "s3_uri": "s3://igvf-files/2025/03/13/68d4397b-d1b9-4617-874e-cd790ce82234/IGVFFI2897TNFT.yaml.gz",
263            "status": "released",
264            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_5381_seqspec.yaml.gz",
265            "upload_status": "validated"
266        },
267        {
268            "@id": "/configuration-files/IGVFFI9503PHEI/",
269            "accession": "IGVFFI9503PHEI",
270            "aliases": [
271                "buenrostro-bernstein:SS-LS_5376_seqspec"
272            ],
273            "content_type": "seqspec",
274            "creation_timestamp": "2025-03-13T17:54:16.435669+00:00",
275            "file_format": "yaml",
276            "file_size": 1288,
277            "href": "/configuration-files/IGVFFI9503PHEI/@@download/IGVFFI9503PHEI.yaml.gz",
278            "s3_uri": "s3://igvf-files/2025/03/13/60d77e96-0c4a-4845-b8dc-938ed6b88981/IGVFFI9503PHEI.yaml.gz",
279            "status": "released",
280            "submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_5376_seqspec.yaml.gz",
281            "upload_status": "validated"
282        }
283    ],
284    "input_for": [
285        "/analysis-sets/IGVFDS2240UYEO/"
286    ],
287    "lab": {
288        "@id": "/labs/jason-buenrostro/",
289        "title": "Jason Buenrostro, Broad"
290    },
291    "multiome_size": 5,
292    "onlist_files": [
293        "/tabular-files/IGVFFI9034HUWG/",
294        "/tabular-files/IGVFFI0400MBIM/"
295    ],
296    "onlist_method": "multi",
297    "preferred_assay_title": "SHARE-seq",
298    "protocols": [
299        "https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
300    ],
301    "related_multiome_datasets": [
302        {
303            "@id": "/measurement-sets/IGVFDS4653HFNR/",
304            "accession": "IGVFDS4653HFNR",
305            "status": "released"
306        },
307        {
308            "@id": "/measurement-sets/IGVFDS1816FCQL/",
309            "accession": "IGVFDS1816FCQL",
310            "status": "released"
311        },
312        {
313            "@id": "/measurement-sets/IGVFDS8623UWKX/",
314            "accession": "IGVFDS8623UWKX",
315            "status": "released"
316        },
317        {
318            "@id": "/measurement-sets/IGVFDS9866LFTQ/",
319            "accession": "IGVFDS9866LFTQ",
320            "status": "released"
321        }
322    ],
323    "release_timestamp": "2025-03-28T21:22:23.877930+00:00",
324    "samples": [
325        {
326            "@id": "/tissues/IGVFSM2881UHTO/",
327            "@type": [
328                "Tissue",
329                "Biosample",
330                "Sample",
331                "Item"
332            ],
333            "accession": "IGVFSM2881UHTO",
334            "aliases": [
335                "buenrostro-bernstein:BioSam 4965_SS-PKR 434"
336            ],
337            "cellular_sub_pool": "SS-PKR 434",
338            "classifications": [
339                "tissue"
340            ],
341            "institutional_certificates": [],
342            "sample_terms": [
343                {
344                    "@id": "/sample-terms/UBERON_0000955/",
345                    "@type": [
346                        "SampleTerm",
347                        "OntologyTerm",
348                        "Item"
349                    ],
350                    "status": "released",
351                    "summary": "brain",
352                    "term_name": "brain"
353                }
354            ],
355            "status": "released",
356            "summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 434)",
357            "taxa": "Mus musculus"
358        }
359    ],
360    "schema_version": "26",
361    "status": "released",
362    "submitted_by": {
363        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
364        "title": "Siddarth Wekhande"
365    },
366    "submitted_files_timestamp": "2025-03-09T15:58:51.233721+00:00",
367    "summary": "single-cell RNA sequencing assay (SHARE-seq)",
368    "uuid": "860ee3e3-d841-4eb6-ba98-264cc49d061f"
369}