IGVFFI0981BEOP

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI0981BEOP/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0981BEOP",
10    "aliases": [
11        "ansuman-satpathy:igvf1_raw_rna_counts_10x2"
12    ],
13    "analysis_step_version": "/analysis-step-versions/072beaf9-db5c-4bb3-9d63-e5cf7ee29dd6/",
14    "assay_titles": [
15        "10x multiome with MULTI-seq"
16    ],
17    "audit": {},
18    "award": {
19        "@id": "/awards/HG011972/",
20        "component": "functional characterization"
21    },
22    "checkfiles_version": "v14",
23    "content_summary": "cell by gene in raw feature barcode matrix",
24    "content_type": "raw feature barcode matrix",
25    "creation_timestamp": "2025-01-28T15:33:41.262017+00:00",
26    "derived_from": [
27        "/sequence-files/IGVFFI0605ORIY/",
28        "/sequence-files/IGVFFI5809HGKP/",
29        "/sequence-files/IGVFFI8903GQTU/",
30        "/sequence-files/IGVFFI7090WVNY/",
31        "/sequence-files/IGVFFI5567DOCL/",
32        "/sequence-files/IGVFFI0877NKND/",
33        "/sequence-files/IGVFFI0339ZACP/",
34        "/sequence-files/IGVFFI2202GIPC/"
35    ],
36    "file_format": "hdf5",
37    "file_format_specifications": [
38        {
39            "@id": "/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/",
40            "description": "Raw RNA count matrix definition for 10x multiome"
41        }
42    ],
43    "file_set": {
44        "@id": "/analysis-sets/IGVFDS1501BSSU/",
45        "@type": [
46            "AnalysisSet",
47            "FileSet",
48            "Item"
49        ],
50        "accession": "IGVFDS1501BSSU",
51        "controlled_access": false,
52        "data_use_limitation_summaries": [
53            "No limitations"
54        ],
55        "file_set_type": "intermediate analysis",
56        "samples": [
57            {
58                "@id": "/multiplexed-samples/IGVFSM8645VILQ/",
59                "@type": [
60                    "MultiplexedSample",
61                    "Sample",
62                    "Item"
63                ],
64                "accession": "IGVFSM8645VILQ",
65                "classifications": [
66                    "cell line",
67                    "multiplexed sample"
68                ],
69                "disease_terms": [],
70                "modifications": [],
71                "sample_terms": [
72                    {
73                        "@id": "/sample-terms/EFO_0002067/",
74                        "status": "released",
75                        "term_name": "K562"
76                    },
77                    {
78                        "@id": "/sample-terms/EFO_0002793/",
79                        "status": "released",
80                        "term_name": "HL-60"
81                    },
82                    {
83                        "@id": "/sample-terms/EFO_0002869/",
84                        "status": "released",
85                        "term_name": "U2OS"
86                    },
87                    {
88                        "@id": "/sample-terms/EFO_0007598/",
89                        "status": "released",
90                        "term_name": "HAP-1"
91                    },
92                    {
93                        "@id": "/sample-terms/EFO_0022838/",
94                        "status": "released",
95                        "term_name": "HUDEP-2"
96                    }
97                ],
98                "status": "released",
99                "summary": "multiplexed sample: Homo sapiens (male) HAP-1 cell line; Homo sapiens (male) HAP-1 cell line; ... and 13 more samples",
100                "taxa": "Homo sapiens",
101                "treatments": []
102            }
103        ],
104        "status": "released",
105        "summary": "single-nucleus ATAC-seq (10x multiome with MULTI-seq), single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)"
106    },
107    "file_size": 204369209,
108    "gene_list_for": [],
109    "href": "/matrix-files/IGVFFI0981BEOP/@@download/IGVFFI0981BEOP.h5",
110    "input_file_for": [],
111    "integrated_in": [],
112    "lab": {
113        "@id": "/labs/ansuman-satpathy/",
114        "title": "Ansuman Satpathy, Stanford"
115    },
116    "loci_list_for": [],
117    "md5sum": "c8139f75505795702df4cb219d7bf630",
118    "principal_dimension": "cell",
119    "quality_metrics": [],
120    "reference_files": [
121        "/reference-files/IGVFFI8311QXYM/",
122        "/reference-files/IGVFFI3944QOJF/"
123    ],
124    "release_timestamp": "2025-03-07T06:04:05.921507+00:00",
125    "s3_uri": "s3://igvf-files/2025/01/28/87c1f000-2910-4d7c-8251-5d6ad77e28bf/IGVFFI0981BEOP.h5",
126    "schema_version": "7",
127    "secondary_dimensions": [
128        "gene"
129    ],
130    "status": "released",
131    "submitted_by": {
132        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
133        "title": "Christopher Mcginnis"
134    },
135    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf1/e1l2_raw_feature_bc_matrix.h5",
136    "summary": "cell by gene in raw feature barcode matrix",
137    "upload_status": "validated",
138    "uuid": "87c1f000-2910-4d7c-8251-5d6ad77e28bf",
139    "workflow": {
140        "@id": "/workflows/IGVFWF1453HVEC/",
141        "name": "Satpathy Cell Ranger",
142        "uniform_pipeline": false
143    }
144}