IGVFFI7758BEID

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI7758BEID/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI7758BEID",
10    "aliases": [
11        "ansuman-satpathy:igvf13_raw_rna_counts_10x4"
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        "INTERNAL_ACTION": [
19            {
20                "category": "mismatched status",
21                "detail": "Released matrix file [IGVFFI7758BEID](/matrix-files/IGVFFI7758BEID/) has in progress subobject reference file [IGVFFI3944QOJF](/reference-files/IGVFFI3944QOJF/).",
22                "level": 30,
23                "level_name": "INTERNAL_ACTION",
24                "name": "audit_item_status",
25                "path": "/matrix-files/IGVFFI7758BEID/"
26            },
27            {
28                "category": "mismatched status",
29                "detail": "Released matrix file [IGVFFI7758BEID](/matrix-files/IGVFFI7758BEID/) has in progress subobject reference file [IGVFFI8311QXYM](/reference-files/IGVFFI8311QXYM/).",
30                "level": 30,
31                "level_name": "INTERNAL_ACTION",
32                "name": "audit_item_status",
33                "path": "/matrix-files/IGVFFI7758BEID/"
34            }
35        ]
36    },
37    "award": {
38        "@id": "/awards/HG011972/",
39        "component": "functional characterization"
40    },
41    "checkfiles_version": "v14",
42    "content_summary": "cell by gene in raw feature barcode matrix",
43    "content_type": "raw feature barcode matrix",
44    "creation_timestamp": "2025-01-28T23:10:26.146746+00:00",
45    "derived_from": [
46        "/sequence-files/IGVFFI1122VRAT/",
47        "/sequence-files/IGVFFI1494SEOZ/",
48        "/sequence-files/IGVFFI0693OPCQ/",
49        "/sequence-files/IGVFFI6869ATIO/",
50        "/sequence-files/IGVFFI8058KVMJ/",
51        "/sequence-files/IGVFFI7978EGKO/",
52        "/sequence-files/IGVFFI3147EJTJ/",
53        "/sequence-files/IGVFFI6077TUWY/",
54        "/sequence-files/IGVFFI2513NIDI/",
55        "/sequence-files/IGVFFI9165RYNI/",
56        "/sequence-files/IGVFFI8790KLTP/",
57        "/sequence-files/IGVFFI0603UADJ/"
58    ],
59    "file_format": "hdf5",
60    "file_format_specifications": [
61        "/documents/e18648f3-63a8-47e0-be86-2670f0cb68f0/"
62    ],
63    "file_set": {
64        "@id": "/analysis-sets/IGVFDS4694DHAU/",
65        "@type": [
66            "AnalysisSet",
67            "FileSet",
68            "Item"
69        ],
70        "accession": "IGVFDS4694DHAU",
71        "file_set_type": "intermediate analysis",
72        "samples": [
73            {
74                "@id": "/multiplexed-samples/IGVFSM4220ALCU/",
75                "@type": [
76                    "MultiplexedSample",
77                    "Sample",
78                    "Item"
79                ],
80                "accession": "IGVFSM4220ALCU",
81                "classifications": [
82                    "tissue",
83                    "multiplexed sample"
84                ],
85                "disease_terms": [
86                    {
87                        "@id": "/phenotype-terms/MONDO_0005010/",
88                        "@type": [
89                            "PhenotypeTerm",
90                            "OntologyTerm",
91                            "Item"
92                        ],
93                        "status": "released",
94                        "summary": "coronary artery disorder",
95                        "term_name": "coronary artery disorder"
96                    }
97                ],
98                "modifications": [],
99                "sample_terms": [
100                    {
101                        "@id": "/sample-terms/UBERON_0001626/",
102                        "status": "released",
103                        "term_name": "left coronary artery"
104                    }
105                ],
106                "status": "released",
107                "summary": "multiplexed sample: Homo sapiens (female, 48 years) left coronary artery tissue associated with coronary artery disorder; Homo sapiens (female, 73 years) left coronary artery tissue associated with coronary artery disorder; ... and 2 more samples",
108                "taxa": "Homo sapiens",
109                "treatments": []
110            }
111        ],
112        "status": "released",
113        "summary": "10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix"
114    },
115    "file_size": 131004101,
116    "gene_list_for": [],
117    "href": "/matrix-files/IGVFFI7758BEID/@@download/IGVFFI7758BEID.h5",
118    "input_file_for": [],
119    "integrated_in": [],
120    "lab": {
121        "@id": "/labs/ansuman-satpathy/",
122        "title": "Ansuman Satpathy, Stanford"
123    },
124    "loci_list_for": [],
125    "md5sum": "176290b3e31227eff2ffe59b31b4d3fd",
126    "principal_dimension": "cell",
127    "quality_metrics": [],
128    "reference_files": [
129        "/reference-files/IGVFFI8311QXYM/",
130        "/reference-files/IGVFFI3944QOJF/"
131    ],
132    "release_timestamp": "2025-03-22T00:44:05.511325+00:00",
133    "s3_uri": "s3://igvf-files/2025/01/28/7790b675-f201-43cd-bba9-0ecab51374ed/IGVFFI7758BEID.h5",
134    "schema_version": "7",
135    "secondary_dimensions": [
136        "gene"
137    ],
138    "status": "released",
139    "submitted_by": {
140        "@id": "/users/353655bc-31a1-4cd9-bac3-c7d34faf722f/",
141        "title": "Christopher Mcginnis"
142    },
143    "submitted_file_name": "/oak/stanford/groups/satpathy/users/backup/cmcg/analysis_sets/igvf13/e13l4_raw_feature_bc_matrix.h5",
144    "summary": "cell by gene in raw feature barcode matrix",
145    "upload_status": "validated",
146    "uuid": "7790b675-f201-43cd-bba9-0ecab51374ed",
147    "workflow": {
148        "@id": "/workflows/IGVFWF1453HVEC/",
149        "name": "Satpathy Cell Ranger",
150        "uniform_pipeline": false
151    }
152}