IGVFDS6753PKAH

released
1{
2    "@context": "/terms/",
3    "@id": "/analysis-sets/IGVFDS6753PKAH/",
4    "@type": [
5        "AnalysisSet",
6        "FileSet",
7        "Item"
8    ],
9    "accession": "IGVFDS6753PKAH",
10    "aliases": [
11        "buenrostro-bernstein:AnalysisSet_BioSam-4965_SS-PKR-436"
12    ],
13    "assay_titles": [
14        "SHARE-seq"
15    ],
16    "audit": {
17        "INTERNAL_ACTION": [
18            {
19                "category": "missing publication",
20                "detail": "Tissue [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
21                "level": 30,
22                "level_name": "INTERNAL_ACTION",
23                "name": "audit_sample_missing_publication",
24                "path": "/tissues/IGVFSM4321WQTD/"
25            },
26            {
27                "category": "missing publication",
28                "detail": "Analysis set [IGVFDS6753PKAH](/analysis-sets/IGVFDS6753PKAH/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
29                "level": 30,
30                "level_name": "INTERNAL_ACTION",
31                "name": "audit_file_set_missing_publication",
32                "path": "/analysis-sets/IGVFDS6753PKAH/"
33            }
34        ],
35        "WARNING": [
36            {
37                "category": "missing age",
38                "detail": "Tissue [IGVFSM4321WQTD](/tissues/IGVFSM4321WQTD/) 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/IGVFSM4321WQTD/"
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": "2025-03-18T19:13:46.116722+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    ],
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98                "/configuration-files/IGVFFI3248DTTM/",
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128                "/sequence-files/IGVFFI3204NMTN/",
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130                "/sequence-files/IGVFFI1173DRYT/",
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132                "/configuration-files/IGVFFI0240SVTR/",
133                "/configuration-files/IGVFFI9596GYXI/",
134                "/configuration-files/IGVFFI3248DTTM/",
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153            "creation_timestamp": "2025-03-27T00:20:16.230321+00:00",
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168                "/sequence-files/IGVFFI4067FRSX/",
169                "/sequence-files/IGVFFI0846GWZX/",
170                "/sequence-files/IGVFFI8647WTOX/",
171                "/sequence-files/IGVFFI3539IOGW/",
172                "/sequence-files/IGVFFI2496FAKM/",
173                "/configuration-files/IGVFFI9471PHWP/",
174                "/configuration-files/IGVFFI7442LQET/",
175                "/configuration-files/IGVFFI9238INBM/",
176                "/configuration-files/IGVFFI4024AMLP/",
177                "/configuration-files/IGVFFI9557CSJM/",
178                "/configuration-files/IGVFFI4735KTCJ/",
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196                "buenrostro-bernstein:IGVFDS6753PKAH_fragment_index"
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214        {
215            "@id": "/index-files/IGVFFI7869TZNC/",
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242            "content_type": "kallisto single cell RNAseq output",
243            "creation_timestamp": "2025-04-01T17:34:04.820641+00:00",
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246                "/sequence-files/IGVFFI3417NQWN/",
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248                "/sequence-files/IGVFFI6997HAKK/",
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250                "/sequence-files/IGVFFI4188BVSG/",
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252                "/sequence-files/IGVFFI2642WOZN/",
253                "/sequence-files/IGVFFI6977ITAT/",
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280            "upload_status": "validated"
281        }
282    ],
283    "functional_assay_mechanisms": [],
284    "input_file_sets": [
285        {
286            "@id": "/measurement-sets/IGVFDS4752BWME/",
287            "accession": "IGVFDS4752BWME",
288            "aliases": [
289                "buenrostro-bernstein:scRNA Lib 611"
290            ],
291            "file_set_type": "experimental data",
292            "status": "released"
293        },
294        {
295            "@id": "/measurement-sets/IGVFDS5083GBBF/",
296            "accession": "IGVFDS5083GBBF",
297            "aliases": [
298                "buenrostro-bernstein:scATAC Lib 1270"
299            ],
300            "file_set_type": "experimental data",
301            "status": "released"
302        },
303        {
304            "@id": "/measurement-sets/IGVFDS6289YQBN/",
305            "accession": "IGVFDS6289YQBN",
306            "aliases": [
307                "buenrostro-bernstein:scRNA Lib 601"
308            ],
309            "file_set_type": "experimental data",
310            "status": "released"
311        },
312        {
313            "@id": "/measurement-sets/IGVFDS7571FXYP/",
314            "accession": "IGVFDS7571FXYP",
315            "aliases": [
316                "buenrostro-bernstein:scRNA Lib 600"
317            ],
318            "file_set_type": "experimental data",
319            "status": "released"
320        },
321        {
322            "@id": "/measurement-sets/IGVFDS5177YHMM/",
323            "accession": "IGVFDS5177YHMM",
324            "aliases": [
325                "buenrostro-bernstein:scRNA Lib 599"
326            ],
327            "file_set_type": "experimental data",
328            "status": "released"
329        }
330    ],
331    "input_for": [],
332    "lab": {
333        "@id": "/labs/jason-buenrostro/",
334        "title": "Jason Buenrostro, Broad"
335    },
336    "protocols": [
337        "https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
338    ],
339    "release_timestamp": "2025-05-07T20:35:02.577609+00:00",
340    "sample_summary": "Mus musculus brain tissue, cellular sub pool(s): SS-PKR 436",
341    "samples": [
342        {
343            "@id": "/tissues/IGVFSM4321WQTD/",
344            "@type": [
345                "Tissue",
346                "Biosample",
347                "Sample",
348                "Item"
349            ],
350            "accession": "IGVFSM4321WQTD",
351            "aliases": [
352                "buenrostro-bernstein:BioSam 4965_SS-PKR 436"
353            ],
354            "cellular_sub_pool": "SS-PKR 436",
355            "classifications": [
356                "tissue"
357            ],
358            "institutional_certificates": [],
359            "sample_terms": [
360                {
361                    "@id": "/sample-terms/UBERON_0000955/",
362                    "@type": [
363                        "SampleTerm",
364                        "OntologyTerm",
365                        "Item"
366                    ],
367                    "status": "released",
368                    "summary": "brain",
369                    "term_name": "brain"
370                }
371            ],
372            "status": "released",
373            "summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 436)",
374            "taxa": "Mus musculus"
375        }
376    ],
377    "schema_version": "10",
378    "status": "released",
379    "submitted_by": {
380        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
381        "title": "Siddarth Wekhande"
382    },
383    "submitted_files_timestamp": "2025-03-27T00:20:16.230321+00:00",
384    "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)",
385    "uuid": "d399c9ab-f223-4c45-af77-35b84e466f31",
386    "workflows": [
387        {
388            "@id": "/workflows/IGVFWF7365VWQV/",
389            "accession": "IGVFWF7365VWQV",
390            "name": "igvf single cell uniform pipeline",
391            "status": "in progress",
392            "uniform_pipeline": true
393        }
394    ]
395}