IGVFDS4681TSQU

1{
2    "@context": "/terms/",
3    "@id": "/analysis-sets/IGVFDS4681TSQU/",
4    "@type": [
5        "AnalysisSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS4681TSQU",
10    "aliases": [
11        "buenrostro-bernstein:AnalysisSet_BioSam-4965_SS-PKR-435"
12    ],
13    "assay_titles": [
14        "SHARE-seq"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "missing publication",
20                "detail": "Analysis set [IGVFDS4681TSQU](/analysis-sets/IGVFDS4681TSQU/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_file_set_missing_publication",
24                "path": "/analysis-sets/IGVFDS4681TSQU/"
25            },
26            {
27                "category": "missing publication",
28                "detail": "Tissue [IGVFSM4121TWUU](/tissues/IGVFSM4121TWUU/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_sample_missing_publication",
32                "path": "/tissues/IGVFSM4121TWUU/"
33            }
34        ],
35        "WARNING": [
36            {
37                "category": "missing age",
38                "detail": "Tissue [IGVFSM4121TWUU](/tissues/IGVFSM4121TWUU/) 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.",
39                "level": 40,
40                "level_name": "WARNING",
41                "name": "audit_biosample_age",
42                "path": "/tissues/IGVFSM4121TWUU/"
43            }
44        ]
45    },
46    "award": {
47        "@id": "/awards/HG011986/",
48        "component": "mapping",
49        "contact_pi": {
50            "@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
51            "title": "Jason Buenrostro"
52        },
53        "title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
54    },
55    "control_for": [],
56    "creation_timestamp": "2025-03-18T19:13:44.141809+00:00",
57    "data_use_limitation_summaries": [
58        "no certificate"
59    ],
60    "donors": [
61        {
62            "@id": "/rodent-donors/IGVFDO9446AKYF/",
63            "accession": "IGVFDO9446AKYF",
64            "aliases": [
65                "buenrostro-bernstein:Donor 2047"
66            ],
67            "sex": "unspecified",
68            "status": "released",
69            "taxa": "Mus musculus"
70        }
71    ],
72    "file_set_type": "intermediate analysis",
73    "files": [
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75            "@id": "/matrix-files/IGVFFI5643DMQY/",
76            "accession": "IGVFFI5643DMQY",
77            "aliases": [
78                "buenrostro-bernstein:IGVFDS4681TSQU_matrix_file"
79            ],
80            "content_type": "sparse gene count matrix",
81            "creation_timestamp": "2025-03-27T00:20:10.673703+00:00",
82            "derived_from": [
83                "/sequence-files/IGVFFI7373BZSM/",
84                "/sequence-files/IGVFFI3364MPWN/",
85                "/sequence-files/IGVFFI6125FKCF/",
86                "/sequence-files/IGVFFI2143XBQS/",
87                "/sequence-files/IGVFFI7237DHQB/",
88                "/sequence-files/IGVFFI4314ECXU/",
89                "/configuration-files/IGVFFI2312GTSH/",
90                "/configuration-files/IGVFFI6864KBCA/",
91                "/configuration-files/IGVFFI8746NBNF/"
92            ],
93            "file_format": "h5ad",
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96            "md5sum": "45880c69ecd93e3bb55ecaba248c1480",
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98            "status": "released",
99            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/f4439f68-837a-444b-9590-bb9736d53f91/call-rna/wf_rna/30a3e8eb-92fe-4b96-a2e4-806002bb4be0/call-kb/SS-PKR-432.h5ad",
100            "upload_status": "validated"
101        },
102        {
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104            "accession": "IGVFFI4228AGRI",
105            "aliases": [
106                "buenrostro-bernstein:IGVFDS4681TSQU_bam"
107            ],
108            "assembly": "GRCm39",
109            "content_type": "alignments",
110            "controlled_access": false,
111            "creation_timestamp": "2025-03-27T01:06:54.145853+00:00",
112            "derived_from": [
113                "/sequence-files/IGVFFI7886EYCG/",
114                "/sequence-files/IGVFFI1194WFRQ/",
115                "/sequence-files/IGVFFI0202KWGE/",
116                "/sequence-files/IGVFFI8371AUNQ/",
117                "/sequence-files/IGVFFI3502EOYB/",
118                "/sequence-files/IGVFFI3420RCKG/",
119                "/sequence-files/IGVFFI1545WPGA/",
120                "/sequence-files/IGVFFI6773USPP/",
121                "/sequence-files/IGVFFI7099FUVH/",
122                "/sequence-files/IGVFFI8918FMWS/",
123                "/configuration-files/IGVFFI7983WCRU/",
124                "/configuration-files/IGVFFI4322UUZN/",
125                "/configuration-files/IGVFFI5373MZTL/",
126                "/configuration-files/IGVFFI9441NKAS/",
127                "/configuration-files/IGVFFI8993BLAC/"
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129            "file_format": "bam",
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134            "status": "released",
135            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/dbe66b20-ce01-402b-bd70-5e9d0d878ab2/call-atac/wf_atac/a6e03b09-d082-40d3-8444-783f3819e0a5/call-generate_bam/SS-PKR-435.bam",
136            "upload_status": "validated"
137        },
138        {
139            "@id": "/index-files/IGVFFI3527QKGP/",
140            "accession": "IGVFFI3527QKGP",
141            "aliases": [
142                "buenrostro-bernstein:IGVFDS4681TSQU_fragment_index"
143            ],
144            "assembly": "GRCm39",
145            "content_type": "index",
146            "controlled_access": false,
147            "creation_timestamp": "2025-03-27T01:21:51.304632+00:00",
148            "derived_from": [
149                "/tabular-files/IGVFFI6974VPAB/"
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156            "status": "released",
157            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/dbe66b20-ce01-402b-bd70-5e9d0d878ab2/call-atac/wf_atac/a6e03b09-d082-40d3-8444-783f3819e0a5/call-generate_fragments/SS-PKR-435.fragments.tsv.gz.tbi",
158            "upload_status": "validated"
159        },
160        {
161            "@id": "/tabular-files/IGVFFI6974VPAB/",
162            "accession": "IGVFFI6974VPAB",
163            "aliases": [
164                "buenrostro-bernstein:IGVFDS4681TSQU_fragments"
165            ],
166            "assembly": "GRCm39",
167            "content_type": "fragments",
168            "controlled_access": false,
169            "creation_timestamp": "2025-03-27T01:19:10.208088+00:00",
170            "derived_from": [
171                "/sequence-files/IGVFFI7886EYCG/",
172                "/sequence-files/IGVFFI1194WFRQ/",
173                "/sequence-files/IGVFFI0202KWGE/",
174                "/sequence-files/IGVFFI8371AUNQ/",
175                "/sequence-files/IGVFFI3502EOYB/",
176                "/sequence-files/IGVFFI3420RCKG/",
177                "/sequence-files/IGVFFI1545WPGA/",
178                "/sequence-files/IGVFFI6773USPP/",
179                "/sequence-files/IGVFFI7099FUVH/",
180                "/sequence-files/IGVFFI8918FMWS/",
181                "/configuration-files/IGVFFI7983WCRU/",
182                "/configuration-files/IGVFFI4322UUZN/",
183                "/configuration-files/IGVFFI5373MZTL/",
184                "/configuration-files/IGVFFI9441NKAS/",
185                "/configuration-files/IGVFFI8993BLAC/"
186            ],
187            "file_format": "bed",
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192            "status": "released",
193            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/dbe66b20-ce01-402b-bd70-5e9d0d878ab2/call-atac/wf_atac/a6e03b09-d082-40d3-8444-783f3819e0a5/call-generate_fragments/SS-PKR-435.fragments.tsv.gz",
194            "upload_status": "validated"
195        },
196        {
197            "@id": "/index-files/IGVFFI6974PJQH/",
198            "accession": "IGVFFI6974PJQH",
199            "aliases": [
200                "buenrostro-bernstein:IGVFDS4681TSQU_bam_index"
201            ],
202            "assembly": "GRCm39",
203            "content_type": "index",
204            "controlled_access": false,
205            "creation_timestamp": "2025-03-27T04:56:40.100637+00:00",
206            "derived_from": [
207                "/alignment-files/IGVFFI4228AGRI/"
208            ],
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214            "status": "released",
215            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/03d491e0-13b3-4b9d-89ce-ae4ebc4c6939/samtools_index_workflow/a9623c24-c57a-49cd-83e7-8528f74c5c2d/call-samtools_index/SS-PKR-435.bam.bai",
216            "upload_status": "validated"
217        },
218        {
219            "@id": "/matrix-files/IGVFFI0035TUYI/",
220            "accession": "IGVFFI0035TUYI",
221            "aliases": [
222                "buenrostro-bernstein:IGVFDS4681TSQU_rna_kb_output_folder_tar_gz"
223            ],
224            "content_type": "kallisto single cell RNAseq output",
225            "creation_timestamp": "2025-04-01T17:19:57.193604+00:00",
226            "derived_from": [
227                "/sequence-files/IGVFFI7373BZSM/",
228                "/sequence-files/IGVFFI3364MPWN/",
229                "/sequence-files/IGVFFI6125FKCF/",
230                "/sequence-files/IGVFFI2143XBQS/",
231                "/sequence-files/IGVFFI7237DHQB/",
232                "/sequence-files/IGVFFI4314ECXU/",
233                "/configuration-files/IGVFFI2312GTSH/",
234                "/configuration-files/IGVFFI6864KBCA/",
235                "/configuration-files/IGVFFI8746NBNF/"
236            ],
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240            "md5sum": "089e52013b0314f9765f13a79aa523c5",
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242            "status": "released",
243            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/dbe66b20-ce01-402b-bd70-5e9d0d878ab2/call-rna/wf_rna/650f1e3d-8c7f-41d5-96f5-a304c31e9308/call-kb/SS-PKR-435.tar.gz",
244            "upload_status": "validated"
245        }
246    ],
247    "functional_assay_mechanisms": [],
248    "input_file_sets": [
249        {
250            "@id": "/measurement-sets/IGVFDS1592MBRQ/",
251            "accession": "IGVFDS1592MBRQ",
252            "aliases": [
253                "buenrostro-bernstein:scRNA Lib 610"
254            ],
255            "file_set_type": "experimental data",
256            "status": "released"
257        },
258        {
259            "@id": "/measurement-sets/IGVFDS8225URBF/",
260            "accession": "IGVFDS8225URBF",
261            "aliases": [
262                "buenrostro-bernstein:scATAC Lib 1269"
263            ],
264            "file_set_type": "experimental data",
265            "status": "released"
266        }
267    ],
268    "input_for": [],
269    "lab": {
270        "@id": "/labs/jason-buenrostro/",
271        "title": "Jason Buenrostro, Broad"
272    },
273    "protocols": [
274        "https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
275    ],
276    "release_timestamp": "2025-05-07T20:35:07.849034+00:00",
277    "sample_summary": "Mus musculus brain tissue, cellular sub pool(s): SS-PKR 435",
278    "samples": [
279        {
280            "@id": "/tissues/IGVFSM4121TWUU/",
281            "@type": [
282                "Tissue",
283                "Biosample",
284                "Sample",
285                "Item"
286            ],
287            "accession": "IGVFSM4121TWUU",
288            "aliases": [
289                "buenrostro-bernstein:BioSam 4965_SS-PKR 435"
290            ],
291            "cellular_sub_pool": "SS-PKR 435",
292            "classifications": [
293                "tissue"
294            ],
295            "institutional_certificates": [],
296            "sample_terms": [
297                {
298                    "@id": "/sample-terms/UBERON_0000955/",
299                    "@type": [
300                        "SampleTerm",
301                        "OntologyTerm",
302                        "Item"
303                    ],
304                    "status": "released",
305                    "summary": "brain",
306                    "term_name": "brain"
307                }
308            ],
309            "status": "released",
310            "summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 435)",
311            "taxa": "Mus musculus"
312        }
313    ],
314    "schema_version": "10",
315    "status": "released",
316    "submitted_by": {
317        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
318        "title": "Siddarth Wekhande"
319    },
320    "submitted_files_timestamp": "2025-03-27T00:20:10.673703+00:00",
321    "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)",
322    "uuid": "44abded0-a60c-44dd-9e44-9b452e15d0b8",
323    "workflows": [
324        {
325            "@id": "/workflows/IGVFWF7365VWQV/",
326            "accession": "IGVFWF7365VWQV",
327            "name": "igvf single cell uniform pipeline",
328            "status": "in progress",
329            "uniform_pipeline": true
330        }
331    ]
332}