IGVFFI8142SBEI

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI8142SBEI/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI8142SBEI",
10    "aliases": [
11        "buenrostro-bernstein:surya-human-organoid-rna-matrix"
12    ],
13    "analysis_step_version": "/analysis-step-versions/45d73e29-280a-4faf-9762-c1b4c655b689/",
14    "assay_titles": [
15        "SHARE-seq"
16    ],
17    "audit": {},
18    "award": {
19        "@id": "/awards/HG011986/",
20        "component": "mapping"
21    },
22    "checkfiles_version": "v17",
23    "content_summary": "cell by gene in sparse gene count matrix",
24    "content_type": "sparse gene count matrix",
25    "creation_timestamp": "2025-03-06T16:51:56.240180+00:00",
26    "derived_from": [
27        "/sequence-files/IGVFFI9831SEGU/",
28        "/sequence-files/IGVFFI8905WBYU/"
29    ],
30    "file_format": "h5ad",
31    "file_format_specifications": [
32        "/documents/cae4f4ad-b937-4694-b5b7-028917c8dbab/"
33    ],
34    "file_set": {
35        "@id": "/analysis-sets/IGVFDS0718WXPI/",
36        "@type": [
37            "AnalysisSet",
38            "FileSet",
39            "Item"
40        ],
41        "accession": "IGVFDS0718WXPI",
42        "file_set_type": "intermediate analysis",
43        "samples": [
44            {
45                "@id": "/in-vitro-systems/IGVFSM7625PGWV/",
46                "@type": [
47                    "InVitroSystem",
48                    "Biosample",
49                    "Sample",
50                    "Item"
51                ],
52                "accession": "IGVFSM7625PGWV",
53                "classifications": [
54                    "organoid"
55                ],
56                "sample_terms": [
57                    {
58                        "@id": "/sample-terms/CL_0011108/",
59                        "status": "released",
60                        "term_name": "colon epithelial cell"
61                    }
62                ],
63                "status": "released",
64                "summary": "Homo sapiens colon epithelial cell organoid induced to colon for 7 days",
65                "targeted_sample_term": {
66                    "@id": "/sample-terms/UBERON_0001155/",
67                    "status": "released",
68                    "term_name": "colon"
69                },
70                "taxa": "Homo sapiens"
71            }
72        ],
73        "status": "released",
74        "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq): fragments, sparse gene count matrix"
75    },
76    "file_size": 63881699,
77    "filtered": false,
78    "gene_list_for": [],
79    "href": "/matrix-files/IGVFFI8142SBEI/@@download/IGVFFI8142SBEI.h5ad",
80    "input_file_for": [],
81    "integrated_in": [],
82    "lab": {
83        "@id": "/labs/jason-buenrostro/",
84        "title": "Jason Buenrostro, Broad"
85    },
86    "loci_list_for": [],
87    "md5sum": "6672db7b863aa8283fc35420d591eef5",
88    "principal_dimension": "cell",
89    "quality_metrics": [],
90    "reference_files": [
91        "/reference-files/IGVFFI0653VCGH/",
92        "/reference-files/IGVFFI7217ZMJZ/"
93    ],
94    "release_timestamp": "2025-03-26T19:25:47.986726+00:00",
95    "s3_uri": "s3://igvf-files/2025/03/06/3a7b359e-39f7-4240-a6ee-703e6299455b/IGVFFI8142SBEI.h5ad",
96    "schema_version": "7",
97    "secondary_dimensions": [
98        "gene"
99    ],
100    "status": "released",
101    "submitted_by": {
102        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
103        "title": "Siddarth Wekhande"
104    },
105    "submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/processed-data/human_organoids.RNA.raw_counts.h5",
106    "summary": "unfiltered cell by gene in sparse gene count matrix",
107    "upload_status": "validated",
108    "uuid": "3a7b359e-39f7-4240-a6ee-703e6299455b",
109    "workflow": {
110        "@id": "/workflows/IGVFWF0507XZOR/",
111        "name": "SHARE-seq-alignmentV2",
112        "uniform_pipeline": false
113    }
114}