IGVFDS0635KHHW

1{
2    "@context": "/terms/",
3    "@id": "/analysis-sets/IGVFDS0635KHHW/",
4    "@type": [
5        "AnalysisSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS0635KHHW",
10    "aliases": [
11        "buenrostro-bernstein:AnalysisSet_BioSam-4561_SS-PKR-130"
12    ],
13    "assay_titles": [
14        "SHARE-seq"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "missing publication",
20                "detail": "Analysis set [IGVFDS0635KHHW](/analysis-sets/IGVFDS0635KHHW/) 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/IGVFDS0635KHHW/"
25            },
26            {
27                "category": "missing publication",
28                "detail": "Tissue [IGVFSM8719IQYM](/tissues/IGVFSM8719IQYM/) 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/IGVFSM8719IQYM/"
33            }
34        ],
35        "NOT_COMPLIANT": [
36            {
37                "category": "missing reference files",
38                "detail": "Analysis set [IGVFDS0635KHHW](/analysis-sets/IGVFDS0635KHHW/) has file(s) with no transcriptome `reference_files`: [IGVFFI0876EPIM](/alignment-files/IGVFFI0876EPIM/)  Analysis set files processed from transcript sequence data are expected to link to a transcriptome reference.",
39                "level": 50,
40                "level_name": "NOT_COMPLIANT",
41                "name": "audit_missing_transcriptome",
42                "path": "/analysis-sets/IGVFDS0635KHHW/"
43            }
44        ],
45        "WARNING": [
46            {
47                "category": "missing age",
48                "detail": "Tissue [IGVFSM8719IQYM](/tissues/IGVFSM8719IQYM/) 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.",
49                "level": 40,
50                "level_name": "WARNING",
51                "name": "audit_biosample_age",
52                "path": "/tissues/IGVFSM8719IQYM/"
53            }
54        ]
55    },
56    "award": {
57        "@id": "/awards/HG011986/",
58        "component": "mapping",
59        "contact_pi": {
60            "@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
61            "title": "Jason Buenrostro"
62        },
63        "title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
64    },
65    "control_for": [],
66    "creation_timestamp": "2025-03-18T19:13:49.147135+00:00",
67    "data_use_limitation_summaries": [
68        "no certificate"
69    ],
70    "donors": [
71        {
72            "@id": "/rodent-donors/IGVFDO1318PLKS/",
73            "accession": "IGVFDO1318PLKS",
74            "aliases": [
75                "bradley-bernstein:Donor 1503",
76                "buenrostro-bernstein:Donor 1503"
77            ],
78            "sex": "female",
79            "status": "released",
80            "taxa": "Mus musculus"
81        }
82    ],
83    "file_set_type": "intermediate analysis",
84    "files": [
85        {
86            "@id": "/matrix-files/IGVFFI9574KLIF/",
87            "accession": "IGVFFI9574KLIF",
88            "aliases": [
89                "buenrostro-bernstein:IGVFDS0635KHHW_matrix_file"
90            ],
91            "content_type": "sparse gene count matrix",
92            "creation_timestamp": "2025-03-27T00:20:06.248611+00:00",
93            "derived_from": [
94                "/sequence-files/IGVFFI0633GTTI/",
95                "/sequence-files/IGVFFI5669BPLY/",
96                "/sequence-files/IGVFFI9424HRUH/",
97                "/sequence-files/IGVFFI2127HVIT/",
98                "/sequence-files/IGVFFI8347HEET/",
99                "/sequence-files/IGVFFI3851WKAQ/",
100                "/sequence-files/IGVFFI8354RXRJ/",
101                "/sequence-files/IGVFFI8558RDPT/",
102                "/sequence-files/IGVFFI7516RQYI/",
103                "/sequence-files/IGVFFI7837YZRO/",
104                "/sequence-files/IGVFFI2540DVGH/",
105                "/sequence-files/IGVFFI4227ZFZB/",
106                "/configuration-files/IGVFFI2318ANJC/",
107                "/configuration-files/IGVFFI2860ERJA/",
108                "/configuration-files/IGVFFI5867RRUA/",
109                "/configuration-files/IGVFFI8020XMTF/",
110                "/configuration-files/IGVFFI6966IHGR/",
111                "/configuration-files/IGVFFI8231RUQE/"
112            ],
113            "file_format": "h5ad",
114            "file_size": 466952224,
115            "href": "/matrix-files/IGVFFI9574KLIF/@@download/IGVFFI9574KLIF.h5ad",
116            "md5sum": "aff82d43a79a787ca5b55b53a47193d3",
117            "s3_uri": "s3://igvf-files/2025/03/27/fe804d90-b942-4d51-8dc6-7a9bad055e75/IGVFFI9574KLIF.h5ad",
118            "status": "released",
119            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/225aed6b-71f4-42ae-989a-45619457db1e/call-rna/wf_rna/e3925ecb-6ccf-4590-9ab7-f43a1719f040/call-kb/SS-PKR-130.h5ad",
120            "upload_status": "validated"
121        },
122        {
123            "@id": "/alignment-files/IGVFFI0876EPIM/",
124            "accession": "IGVFFI0876EPIM",
125            "aliases": [
126                "buenrostro-bernstein:IGVFDS0635KHHW_bam"
127            ],
128            "assembly": "GRCm39",
129            "content_type": "alignments",
130            "controlled_access": false,
131            "creation_timestamp": "2025-03-27T01:05:41.267224+00:00",
132            "derived_from": [
133                "/sequence-files/IGVFFI7508PACU/",
134                "/sequence-files/IGVFFI2472BMSD/",
135                "/sequence-files/IGVFFI2829RADG/",
136                "/sequence-files/IGVFFI4706YQDR/",
137                "/sequence-files/IGVFFI2975AWSJ/",
138                "/sequence-files/IGVFFI1001KYTA/",
139                "/sequence-files/IGVFFI4386BDER/",
140                "/sequence-files/IGVFFI4385PBLT/",
141                "/sequence-files/IGVFFI9352PGPF/",
142                "/sequence-files/IGVFFI9343KESJ/",
143                "/sequence-files/IGVFFI6665GUBQ/",
144                "/sequence-files/IGVFFI4364SHWE/",
145                "/configuration-files/IGVFFI2356MCSL/",
146                "/configuration-files/IGVFFI1054JKKD/",
147                "/configuration-files/IGVFFI9756RDEZ/",
148                "/configuration-files/IGVFFI4215EIYQ/",
149                "/configuration-files/IGVFFI5892NIPL/",
150                "/configuration-files/IGVFFI3943XKRN/"
151            ],
152            "file_format": "bam",
153            "file_size": 3023634110,
154            "href": "/alignment-files/IGVFFI0876EPIM/@@download/IGVFFI0876EPIM.bam",
155            "md5sum": "58e170bd465d25133df00a952a5ba77f",
156            "s3_uri": "s3://igvf-files/2025/03/27/23c3e7cd-6e19-4b66-89c0-37ff90d25f12/IGVFFI0876EPIM.bam",
157            "status": "released",
158            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/225aed6b-71f4-42ae-989a-45619457db1e/call-atac/wf_atac/0187a2d3-be98-4679-aa42-6e9d43d160ba/call-generate_bam/SS-PKR-130.bam",
159            "upload_status": "validated"
160        },
161        {
162            "@id": "/index-files/IGVFFI3423JHNW/",
163            "accession": "IGVFFI3423JHNW",
164            "aliases": [
165                "buenrostro-bernstein:IGVFDS0635KHHW_fragment_index"
166            ],
167            "assembly": "GRCm39",
168            "content_type": "index",
169            "controlled_access": false,
170            "creation_timestamp": "2025-03-27T01:20:53.497682+00:00",
171            "derived_from": [
172                "/tabular-files/IGVFFI6441PWQZ/"
173            ],
174            "file_format": "tbi",
175            "file_size": 557331,
176            "href": "/index-files/IGVFFI3423JHNW/@@download/IGVFFI3423JHNW.tbi",
177            "md5sum": "299071ff96c79409dd7ecb253ec1ff2d",
178            "s3_uri": "s3://igvf-files/2025/03/27/0e2e35f8-937c-4a35-9224-df8192cc7f23/IGVFFI3423JHNW.tbi",
179            "status": "released",
180            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/225aed6b-71f4-42ae-989a-45619457db1e/call-atac/wf_atac/0187a2d3-be98-4679-aa42-6e9d43d160ba/call-generate_fragments/SS-PKR-130.fragments.tsv.gz.tbi",
181            "upload_status": "validated"
182        },
183        {
184            "@id": "/tabular-files/IGVFFI6441PWQZ/",
185            "accession": "IGVFFI6441PWQZ",
186            "aliases": [
187                "buenrostro-bernstein:IGVFDS0635KHHW_fragments"
188            ],
189            "assembly": "GRCm39",
190            "content_type": "fragments",
191            "controlled_access": false,
192            "creation_timestamp": "2025-03-27T01:17:50.137925+00:00",
193            "derived_from": [
194                "/sequence-files/IGVFFI7508PACU/",
195                "/sequence-files/IGVFFI2472BMSD/",
196                "/sequence-files/IGVFFI2829RADG/",
197                "/sequence-files/IGVFFI4706YQDR/",
198                "/sequence-files/IGVFFI2975AWSJ/",
199                "/sequence-files/IGVFFI1001KYTA/",
200                "/sequence-files/IGVFFI4386BDER/",
201                "/sequence-files/IGVFFI4385PBLT/",
202                "/sequence-files/IGVFFI9352PGPF/",
203                "/sequence-files/IGVFFI9343KESJ/",
204                "/sequence-files/IGVFFI6665GUBQ/",
205                "/sequence-files/IGVFFI4364SHWE/",
206                "/configuration-files/IGVFFI2356MCSL/",
207                "/configuration-files/IGVFFI1054JKKD/",
208                "/configuration-files/IGVFFI9756RDEZ/",
209                "/configuration-files/IGVFFI4215EIYQ/",
210                "/configuration-files/IGVFFI5892NIPL/",
211                "/configuration-files/IGVFFI3943XKRN/"
212            ],
213            "file_format": "bed",
214            "file_size": 422574093,
215            "href": "/tabular-files/IGVFFI6441PWQZ/@@download/IGVFFI6441PWQZ.bed.gz",
216            "md5sum": "55ba33ad65cbc0d3724bd37355a26595",
217            "s3_uri": "s3://igvf-files/2025/03/27/e0534e32-2e4e-48b3-82c8-f6fc5b0b8cb5/IGVFFI6441PWQZ.bed.gz",
218            "status": "released",
219            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/225aed6b-71f4-42ae-989a-45619457db1e/call-atac/wf_atac/0187a2d3-be98-4679-aa42-6e9d43d160ba/call-generate_fragments/SS-PKR-130.fragments.tsv.gz",
220            "upload_status": "validated"
221        },
222        {
223            "@id": "/index-files/IGVFFI3983XJWW/",
224            "accession": "IGVFFI3983XJWW",
225            "aliases": [
226                "buenrostro-bernstein:IGVFDS0635KHHW_bam_index"
227            ],
228            "assembly": "GRCm39",
229            "content_type": "index",
230            "controlled_access": false,
231            "creation_timestamp": "2025-03-27T04:42:29.504742+00:00",
232            "derived_from": [
233                "/alignment-files/IGVFFI0876EPIM/"
234            ],
235            "file_format": "bai",
236            "file_size": 2235368,
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240            "status": "released",
241            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/03d491e0-13b3-4b9d-89ce-ae4ebc4c6939/samtools_index_workflow/ab25b7f7-ce4c-4b60-9096-685cd833fc62/call-samtools_index/SS-PKR-130.bam.bai",
242            "upload_status": "validated"
243        },
244        {
245            "@id": "/matrix-files/IGVFFI9304NYFI/",
246            "accession": "IGVFFI9304NYFI",
247            "aliases": [
248                "buenrostro-bernstein:IGVFDS0635KHHW_rna_kb_output_folder_tar_gz"
249            ],
250            "content_type": "comprehensive gene count matrix",
251            "creation_timestamp": "2025-04-01T16:06:54.656564+00:00",
252            "derived_from": [
253                "/sequence-files/IGVFFI0633GTTI/",
254                "/sequence-files/IGVFFI5669BPLY/",
255                "/sequence-files/IGVFFI9424HRUH/",
256                "/sequence-files/IGVFFI2127HVIT/",
257                "/sequence-files/IGVFFI8347HEET/",
258                "/sequence-files/IGVFFI3851WKAQ/",
259                "/sequence-files/IGVFFI8354RXRJ/",
260                "/sequence-files/IGVFFI8558RDPT/",
261                "/sequence-files/IGVFFI7516RQYI/",
262                "/sequence-files/IGVFFI7837YZRO/",
263                "/sequence-files/IGVFFI2540DVGH/",
264                "/sequence-files/IGVFFI4227ZFZB/",
265                "/configuration-files/IGVFFI2318ANJC/",
266                "/configuration-files/IGVFFI2860ERJA/",
267                "/configuration-files/IGVFFI5867RRUA/",
268                "/configuration-files/IGVFFI8020XMTF/",
269                "/configuration-files/IGVFFI6966IHGR/",
270                "/configuration-files/IGVFFI8231RUQE/"
271            ],
272            "file_format": "tar",
273            "file_size": 2573653240,
274            "href": "/matrix-files/IGVFFI9304NYFI/@@download/IGVFFI9304NYFI.tar.gz",
275            "md5sum": "76a303348dee35f500df84a707677d64",
276            "s3_uri": "s3://igvf-files/2025/04/01/5de5cbd9-f63e-4111-bc37-e938d411c21f/IGVFFI9304NYFI.tar.gz",
277            "status": "released",
278            "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/a6d4a8e2-651e-421f-ae34-bfdf4cf1f42e/single_cell_pipeline/225aed6b-71f4-42ae-989a-45619457db1e/call-rna/wf_rna/e3925ecb-6ccf-4590-9ab7-f43a1719f040/call-kb/SS-PKR-130.tar.gz",
279            "upload_status": "validated"
280        }
281    ],
282    "functional_assay_mechanisms": [],
283    "input_file_sets": [
284        {
285            "@id": "/measurement-sets/IGVFDS8556WPGM/",
286            "accession": "IGVFDS8556WPGM",
287            "aliases": [
288                "bradley-bernstein:scATAC Lib 114",
289                "buenrostro-bernstein:scATAC Lib 114"
290            ],
291            "file_set_type": "experimental data",
292            "status": "released"
293        },
294        {
295            "@id": "/measurement-sets/IGVFDS3032KHHX/",
296            "accession": "IGVFDS3032KHHX",
297            "aliases": [
298                "bradley-bernstein:scATAC Lib 113",
299                "buenrostro-bernstein:scATAC Lib 113"
300            ],
301            "file_set_type": "experimental data",
302            "status": "released"
303        },
304        {
305            "@id": "/measurement-sets/IGVFDS4704VICJ/",
306            "accession": "IGVFDS4704VICJ",
307            "aliases": [
308                "bradley-bernstein:scATAC Lib 112",
309                "buenrostro-bernstein:scATAC Lib 112"
310            ],
311            "file_set_type": "experimental data",
312            "status": "released"
313        },
314        {
315            "@id": "/measurement-sets/IGVFDS9693BTRP/",
316            "accession": "IGVFDS9693BTRP",
317            "aliases": [
318                "bradley-bernstein:scRNA Lib 75",
319                "buenrostro-bernstein:scRNA Lib 75"
320            ],
321            "file_set_type": "experimental data",
322            "status": "released"
323        },
324        {
325            "@id": "/measurement-sets/IGVFDS0877CWMW/",
326            "accession": "IGVFDS0877CWMW",
327            "aliases": [
328                "bradley-bernstein:scRNA Lib 74",
329                "buenrostro-bernstein:scRNA Lib 74"
330            ],
331            "file_set_type": "experimental data",
332            "status": "released"
333        },
334        {
335            "@id": "/measurement-sets/IGVFDS6361NSJR/",
336            "accession": "IGVFDS6361NSJR",
337            "aliases": [
338                "bradley-bernstein:scRNA Lib 73",
339                "buenrostro-bernstein:scRNA Lib 73"
340            ],
341            "file_set_type": "experimental data",
342            "status": "released"
343        }
344    ],
345    "input_for": [],
346    "lab": {
347        "@id": "/labs/jason-buenrostro/",
348        "title": "Jason Buenrostro, Broad"
349    },
350    "protocols": [
351        "https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
352    ],
353    "release_timestamp": "2025-05-07T20:34:58.616930+00:00",
354    "sample_summary": "Mus musculus brain tissue",
355    "samples": [
356        {
357            "@id": "/tissues/IGVFSM8719IQYM/",
358            "@type": [
359                "Tissue",
360                "Biosample",
361                "Sample",
362                "Item"
363            ],
364            "accession": "IGVFSM8719IQYM",
365            "aliases": [
366                "bradley-bernstein:BioSam 4561_SS-PKR 130",
367                "buenrostro-bernstein:BioSam 4561_SS-PKR 130"
368            ],
369            "cellular_sub_pool": "SS-PKR 130",
370            "classifications": [
371                "tissue"
372            ],
373            "institutional_certificates": [],
374            "sample_terms": [
375                {
376                    "@id": "/sample-terms/UBERON_0000955/",
377                    "@type": [
378                        "SampleTerm",
379                        "OntologyTerm",
380                        "Item"
381                    ],
382                    "status": "released",
383                    "summary": "brain",
384                    "term_name": "brain"
385                }
386            ],
387            "status": "released",
388            "summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)",
389            "taxa": "Mus musculus"
390        }
391    ],
392    "schema_version": "9",
393    "status": "released",
394    "submitted_by": {
395        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
396        "title": "Siddarth Wekhande"
397    },
398    "submitted_files_timestamp": "2025-03-27T00:20:06.248611+00:00",
399    "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)",
400    "uuid": "ec1c385d-2b23-4943-aa22-bd6cb65bbe9e",
401    "workflows": [
402        {
403            "@id": "/workflows/IGVFWF7365VWQV/",
404            "accession": "IGVFWF7365VWQV",
405            "name": "igvf single cell uniform pipeline",
406            "status": "in progress",
407            "uniform_pipeline": true
408        }
409    ]
410}