IGVFFI0400PXGY

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI0400PXGY/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0400PXGY",
10    "aliases": [
11        "buenrostro-bernstein:IGVFDS2240UYEO_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": "2025-03-27T00:20:14.798515+00:00",
26    "derived_from": [
27        "/sequence-files/IGVFFI3151GLAE/",
28        "/sequence-files/IGVFFI8294TYFC/",
29        "/sequence-files/IGVFFI5362KWQZ/",
30        "/sequence-files/IGVFFI7735CDGU/",
31        "/sequence-files/IGVFFI1620FHAB/",
32        "/sequence-files/IGVFFI6227GVAN/",
33        "/sequence-files/IGVFFI0309CZNF/",
34        "/sequence-files/IGVFFI1199GCIN/",
35        "/sequence-files/IGVFFI0834RTNI/",
36        "/sequence-files/IGVFFI1562DYER/",
37        "/sequence-files/IGVFFI8794VJYW/",
38        "/sequence-files/IGVFFI6526BCJI/",
39        "/sequence-files/IGVFFI3521DARM/",
40        "/sequence-files/IGVFFI9110GXHY/",
41        "/sequence-files/IGVFFI4731HIPN/",
42        "/sequence-files/IGVFFI2221EFRC/",
43        "/sequence-files/IGVFFI4949HHAZ/",
44        "/sequence-files/IGVFFI9814XYUH/",
45        "/configuration-files/IGVFFI5292TPOX/",
46        "/configuration-files/IGVFFI0432LITC/",
47        "/configuration-files/IGVFFI9503PHEI/",
48        "/configuration-files/IGVFFI2764HFQD/",
49        "/configuration-files/IGVFFI2665KLTA/",
50        "/configuration-files/IGVFFI5881EHHY/",
51        "/configuration-files/IGVFFI2897TNFT/",
52        "/configuration-files/IGVFFI2622TPEI/",
53        "/configuration-files/IGVFFI2689KSCB/"
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55    "file_format": "h5ad",
56    "file_format_specifications": [
57        {
58            "@id": "/documents/6a6baaba-6bea-4283-9eb5-a1b4cd4a3a67/",
59            "description": "Specification of matrix h5 generated by https://github.com/IGVF/single-cell-pipeline"
60        }
61    ],
62    "file_set": {
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64        "@type": [
65            "AnalysisSet",
66            "FileSet",
67            "Item"
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69        "accession": "IGVFDS2240UYEO",
70        "data_use_limitation_summaries": [
71            "no certificate"
72        ],
73        "file_set_type": "intermediate analysis",
74        "samples": [
75            {
76                "@id": "/tissues/IGVFSM2881UHTO/",
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79                    "Biosample",
80                    "Sample",
81                    "Item"
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83                "accession": "IGVFSM2881UHTO",
84                "classifications": [
85                    "tissue"
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87                "sample_terms": [
88                    {
89                        "@id": "/sample-terms/UBERON_0000955/",
90                        "status": "released",
91                        "term_name": "brain"
92                    }
93                ],
94                "status": "released",
95                "summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 434)",
96                "taxa": "Mus musculus"
97            }
98        ],
99        "status": "released",
100        "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)"
101    },
102    "file_size": 976368272,
103    "filtered": false,
104    "gene_list_for": [],
105    "href": "/matrix-files/IGVFFI0400PXGY/@@download/IGVFFI0400PXGY.h5ad",
106    "input_file_for": [],
107    "integrated_in": [],
108    "lab": {
109        "@id": "/labs/jason-buenrostro/",
110        "title": "Jason Buenrostro, Broad"
111    },
112    "loci_list_for": [],
113    "md5sum": "f4ea7186d5dfcd7a880607dd41d265e3",
114    "principal_dimension": "cell",
115    "quality_metrics": [
116        "/single-cell-rna-seq-quality-metrics/3d1d758c-b965-43dc-b6cf-36f517a1e65a/"
117    ],
118    "reference_files": [
119        "/reference-files/IGVFFI5078MNED/",
120        "/reference-files/IGVFFI5593VLWB/"
121    ],
122    "release_timestamp": "2025-05-07T20:34:57.549535+00:00",
123    "s3_uri": "s3://igvf-files/2025/03/27/ff67b4e1-8662-4f22-9771-e949a3b91886/IGVFFI0400PXGY.h5ad",
124    "schema_version": "8",
125    "secondary_dimensions": [
126        "gene"
127    ],
128    "status": "released",
129    "submitted_by": {
130        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
131        "title": "Siddarth Wekhande"
132    },
133    "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.h5ad",
134    "summary": "unfiltered cell by gene in sparse gene count matrix",
135    "upload_status": "validated",
136    "uuid": "ff67b4e1-8662-4f22-9771-e949a3b91886",
137    "workflow": {
138        "@id": "/workflows/IGVFWF7365VWQV/",
139        "name": "igvf single cell uniform pipeline",
140        "uniform_pipeline": true
141    }
142}