IGVFFI8130LOBS

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/matrix-files/IGVFFI8130LOBS/",
4    "@type": [
5        "MatrixFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI8130LOBS",
10    "aliases": [
11        "buenrostro-bernstein:IGVFDS2240UYEO_rna_kb_output_folder_tar_gz"
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_md5sum": "43f98045535abae1adfedd7308b7ca0a",
24    "content_summary": "cell by gene in kallisto single cell RNAseq output",
25    "content_type": "kallisto single cell RNAseq output",
26    "creation_timestamp": "2025-04-01T17:06:34.286325+00:00",
27    "derived_from": [
28        "/sequence-files/IGVFFI3151GLAE/",
29        "/sequence-files/IGVFFI8294TYFC/",
30        "/sequence-files/IGVFFI5362KWQZ/",
31        "/sequence-files/IGVFFI7735CDGU/",
32        "/sequence-files/IGVFFI1620FHAB/",
33        "/sequence-files/IGVFFI6227GVAN/",
34        "/sequence-files/IGVFFI0309CZNF/",
35        "/sequence-files/IGVFFI1199GCIN/",
36        "/sequence-files/IGVFFI0834RTNI/",
37        "/sequence-files/IGVFFI1562DYER/",
38        "/sequence-files/IGVFFI8794VJYW/",
39        "/sequence-files/IGVFFI6526BCJI/",
40        "/sequence-files/IGVFFI3521DARM/",
41        "/sequence-files/IGVFFI9110GXHY/",
42        "/sequence-files/IGVFFI4731HIPN/",
43        "/sequence-files/IGVFFI2221EFRC/",
44        "/sequence-files/IGVFFI4949HHAZ/",
45        "/sequence-files/IGVFFI9814XYUH/",
46        "/configuration-files/IGVFFI5292TPOX/",
47        "/configuration-files/IGVFFI0432LITC/",
48        "/configuration-files/IGVFFI9503PHEI/",
49        "/configuration-files/IGVFFI2764HFQD/",
50        "/configuration-files/IGVFFI2665KLTA/",
51        "/configuration-files/IGVFFI5881EHHY/",
52        "/configuration-files/IGVFFI2897TNFT/",
53        "/configuration-files/IGVFFI2622TPEI/",
54        "/configuration-files/IGVFFI2689KSCB/"
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56    "file_format": "tar",
57    "file_format_specifications": [
58        {
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60            "description": "Specification of matrix tar generated by https://github.com/IGVF/single-cell-pipeline"
61        },
62        {
63            "@id": "/documents/2ebce0a7-4990-4d22-8aad-b896f42f49e5/",
64            "description": "Specification of each mtx and txt file in matrix tar file from single cell RNA uniform pipeline"
65        }
66    ],
67    "file_set": {
68        "@id": "/analysis-sets/IGVFDS2240UYEO/",
69        "@type": [
70            "AnalysisSet",
71            "FileSet",
72            "Item"
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74        "accession": "IGVFDS2240UYEO",
75        "data_use_limitation_summaries": [
76            "no certificate"
77        ],
78        "file_set_type": "intermediate analysis",
79        "samples": [
80            {
81                "@id": "/tissues/IGVFSM2881UHTO/",
82                "@type": [
83                    "Tissue",
84                    "Biosample",
85                    "Sample",
86                    "Item"
87                ],
88                "accession": "IGVFSM2881UHTO",
89                "classifications": [
90                    "tissue"
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92                "sample_terms": [
93                    {
94                        "@id": "/sample-terms/UBERON_0000955/",
95                        "status": "released",
96                        "term_name": "brain"
97                    }
98                ],
99                "status": "released",
100                "summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 434)",
101                "taxa": "Mus musculus"
102            }
103        ],
104        "status": "released",
105        "summary": "single-cell ATAC-seq (SHARE-seq), single-cell RNA sequencing assay (SHARE-seq)"
106    },
107    "file_size": 5454016178,
108    "filtered": false,
109    "gene_list_for": [],
110    "href": "/matrix-files/IGVFFI8130LOBS/@@download/IGVFFI8130LOBS.tar.gz",
111    "input_file_for": [],
112    "integrated_in": [],
113    "lab": {
114        "@id": "/labs/jason-buenrostro/",
115        "title": "Jason Buenrostro, Broad"
116    },
117    "loci_list_for": [],
118    "md5sum": "37a8b4c6ddef666d75ac5a3eee1a857f",
119    "notes": "This file's content_type was comprehensive gene count matrix, but has been upgraded to kallisto single cell RNAseq output.",
120    "principal_dimension": "cell",
121    "quality_metrics": [
122        "/single-cell-rna-seq-quality-metrics/3d1d758c-b965-43dc-b6cf-36f517a1e65a/"
123    ],
124    "reference_files": [
125        "/reference-files/IGVFFI5078MNED/"
126    ],
127    "release_timestamp": "2025-05-07T20:34:57.861935+00:00",
128    "s3_uri": "s3://igvf-files/2025/04/01/3b1067b4-c773-4efa-b7d9-ecd317d96de7/IGVFFI8130LOBS.tar.gz",
129    "schema_version": "8",
130    "secondary_dimensions": [
131        "gene"
132    ],
133    "status": "released",
134    "submitted_by": {
135        "@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
136        "title": "Siddarth Wekhande"
137    },
138    "submitted_file_name": "gs://fc-9649faf8-a4ec-4ca4-a975-498a1707d03c/submissions/1d455597-b132-452b-8b75-bf2db8c76d2e/single_cell_pipeline/053cebc3-3088-4281-87d1-65fca1fcb4ea/call-rna/wf_rna/d1a40407-23d0-447c-805b-7a9c987f8505/call-kb/SS-PKR-434.tar.gz",
139    "summary": "unfiltered cell by gene in kallisto single cell RNAseq output",
140    "upload_status": "validated",
141    "uuid": "3b1067b4-c773-4efa-b7d9-ecd317d96de7",
142    "workflow": {
143        "@id": "/workflows/IGVFWF7365VWQV/",
144        "name": "igvf single cell uniform pipeline",
145        "uniform_pipeline": true
146    }
147}