IGVFFI9942FRQQ

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/configuration-files/IGVFFI9942FRQQ/",
4    "@type": [
5        "ConfigurationFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9942FRQQ",
10    "aliases": [
11        "jesse-engreitz:seqspecfile_CRUDO_SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65"
12    ],
13    "assay_titles": [
14        "CRISPR FlowFISH screen"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011972/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "6f736d87ffdf0a24f73b179dd8598ced",
22    "content_type": "seqspec",
23    "creation_timestamp": "2024-06-11T20:38:12.428265+00:00",
24    "file_format": "yaml",
25    "file_set": {
26        "@id": "/measurement-sets/IGVFDS0884TWTU/",
27        "@type": [
28            "MeasurementSet",
29            "FileSet",
30            "Item"
31        ],
32        "accession": "IGVFDS0884TWTU",
33        "assay_term": {
34            "@id": "/assay-terms/OBI_0003661/",
35            "term_name": "in vitro CRISPR screen using flow cytometry"
36        },
37        "file_set_type": "experimental data",
38        "samples": [
39            {
40                "@id": "/in-vitro-systems/IGVFSM7435FSSP/",
41                "@type": [
42                    "InVitroSystem",
43                    "Biosample",
44                    "Sample",
45                    "Item"
46                ],
47                "accession": "IGVFSM7435FSSP",
48                "classifications": [
49                    "cell line"
50                ],
51                "modifications": [
52                    {
53                        "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
54                        "modality": "interference",
55                        "status": "released",
56                        "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
57                    },
58                    {
59                        "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
60                        "modality": "degradation",
61                        "status": "released",
62                        "summary": "inactive AID system targeting RAD21"
63                    }
64                ],
65                "sample_terms": [
66                    {
67                        "@id": "/sample-terms/EFO_0002824/",
68                        "status": "released",
69                        "term_name": "HCT116"
70                    }
71                ],
72                "status": "released",
73                "summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin E for 80-90% expression of SSFA2) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
74                "taxa": "Homo sapiens"
75            }
76        ],
77        "status": "released",
78        "summary": "mixed CRISPR FlowFISH screen sorted on the expression of ITPRID2 integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
79    },
80    "file_size": 911,
81    "gene_list_for": [],
82    "href": "/configuration-files/IGVFFI9942FRQQ/@@download/IGVFFI9942FRQQ.yaml.gz",
83    "input_file_for": [],
84    "integrated_in": [],
85    "lab": {
86        "@id": "/labs/jesse-engreitz/",
87        "title": "Jesse Engreitz, Stanford"
88    },
89    "loci_list_for": [],
90    "md5sum": "2f9e13b2f297ba50ee3d0817f22efb15",
91    "quality_metrics": [],
92    "release_timestamp": "2024-07-10T20:24:11.426408+00:00",
93    "s3_uri": "s3://igvf-files/2024/06/11/a4ea4770-a7e1-4385-90be-d37fa85508df/IGVFFI9942FRQQ.yaml.gz",
94    "schema_version": "7",
95    "seqspec_of": [
96        "/sequence-files/IGVFFI3035ARRF/"
97    ],
98    "status": "released",
99    "submitted_by": {
100        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
101        "title": "Benjamin Doughty"
102    },
103    "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/guideseq.out.SSFA2-Auxin0hrs-FF1-BinE-PCR4-Rep1_S65.yaml",
104    "summary": "seqspec of IGVFFI3035ARRF",
105    "upload_status": "validation exempted",
106    "uuid": "a4ea4770-a7e1-4385-90be-d37fa85508df",
107    "validate_onlist_files": false
108}