IGVFFI9574KLIF

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI9574KLIF/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9574KLIF",
10    "aliases": [
11        "buenrostro-bernstein:IGVFDS0635KHHW_matrix_file"
12    ],
13    "analysis_step_version": "/analysis-step-versions/9c457b9f-fc6d-4cf1-b249-218827e9b449/",
14    "assay_titles": [
15        "SHARE-seq"
16    ],
17    "audit": {},
18    "award": {
19        "@id": "/awards/HG011986/",
20        "component": "mapping"
21    },
22    "checkfiles_version": "v20",
23    "content_summary": "cell by gene in sparse gene count matrix",
24    "content_type": "sparse gene count matrix",
25    "creation_timestamp": "2025-03-27T00:20:06.248611+00:00",
26    "derived_from": [
27        "/sequence-files/IGVFFI0633GTTI/",
28        "/sequence-files/IGVFFI5669BPLY/",
29        "/sequence-files/IGVFFI9424HRUH/",
30        "/sequence-files/IGVFFI2127HVIT/",
31        "/sequence-files/IGVFFI8347HEET/",
32        "/sequence-files/IGVFFI3851WKAQ/",
33        "/sequence-files/IGVFFI8354RXRJ/",
34        "/sequence-files/IGVFFI8558RDPT/",
35        "/sequence-files/IGVFFI7516RQYI/",
36        "/sequence-files/IGVFFI7837YZRO/",
37        "/sequence-files/IGVFFI2540DVGH/",
38        "/sequence-files/IGVFFI4227ZFZB/",
39        "/configuration-files/IGVFFI2318ANJC/",
40        "/configuration-files/IGVFFI2860ERJA/",
41        "/configuration-files/IGVFFI5867RRUA/",
42        "/configuration-files/IGVFFI8020XMTF/",
43        "/configuration-files/IGVFFI6966IHGR/",
44        "/configuration-files/IGVFFI8231RUQE/"
45    ],
46    "file_format": "h5ad",
47    "file_format_specifications": [
48        {
49            "@id": "/documents/6a6baaba-6bea-4283-9eb5-a1b4cd4a3a67/",
50            "description": "Specification of matrix h5 generated by https://github.com/IGVF/single-cell-pipeline"
51        }
52    ],
53    "file_set": {
54        "@id": "/analysis-sets/IGVFDS0635KHHW/",
55        "@type": [
56            "AnalysisSet",
57            "FileSet",
58            "Item"
59        ],
60        "accession": "IGVFDS0635KHHW",
61        "data_use_limitation_summaries": [
62            "no certificate"
63        ],
64        "file_set_type": "intermediate analysis",
65        "samples": [
66            {
67                "@id": "/tissues/IGVFSM8719IQYM/",
68                "@type": [
69                    "Tissue",
70                    "Biosample",
71                    "Sample",
72                    "Item"
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74                "accession": "IGVFSM8719IQYM",
75                "classifications": [
76                    "tissue"
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78                "sample_terms": [
79                    {
80                        "@id": "/sample-terms/UBERON_0000955/",
81                        "status": "released",
82                        "term_name": "brain"
83                    }
84                ],
85                "status": "released",
86                "summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 130)",
87                "taxa": "Mus musculus"
88            }
89        ],
90        "status": "released",
91        "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)"
92    },
93    "file_size": 466952224,
94    "filtered": false,
95    "gene_list_for": [],
96    "href": "/matrix-files/IGVFFI9574KLIF/@@download/IGVFFI9574KLIF.h5ad",
97    "input_file_for": [],
98    "integrated_in": [],
99    "lab": {
100        "@id": "/labs/jason-buenrostro/",
101        "title": "Jason Buenrostro, Broad"
102    },
103    "loci_list_for": [],
104    "md5sum": "aff82d43a79a787ca5b55b53a47193d3",
105    "principal_dimension": "cell",
106    "quality_metrics": [
107        "/single-cell-rna-seq-quality-metrics/3bf6baac-6b4a-46fe-bbfe-84091bc5d077/"
108    ],
109    "reference_files": [
110        "/reference-files/IGVFFI5078MNED/",
111        "/reference-files/IGVFFI5593VLWB/"
112    ],
113    "release_timestamp": "2025-05-07T20:34:59.729462+00:00",
114    "s3_uri": "s3://igvf-files/2025/03/27/fe804d90-b942-4d51-8dc6-7a9bad055e75/IGVFFI9574KLIF.h5ad",
115    "schema_version": "7",
116    "secondary_dimensions": [
117        "gene"
118    ],
119    "status": "released",
120    "submitted_by": {
121        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
122        "title": "Siddarth Wekhande"
123    },
124    "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",
125    "summary": "unfiltered cell by gene in sparse gene count matrix",
126    "upload_status": "validated",
127    "uuid": "fe804d90-b942-4d51-8dc6-7a9bad055e75",
128    "workflow": {
129        "@id": "/workflows/IGVFWF7365VWQV/",
130        "name": "igvf single cell uniform pipeline",
131        "uniform_pipeline": true
132    }
133}