IGVFFI5301LVOU

released
validation exempted
1{
2    "@context": "/terms/",
3    "@id": "/configuration-files/IGVFFI5301LVOU/",
4    "@type": [
5        "ConfigurationFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI5301LVOU",
10    "aliases": [
11        "jesse-engreitz:seqspecfile_crispr_CRUDO_TAPseq_Auxin6hrs-Rep2-S4"
12    ],
13    "assay_titles": [
14        "TAP-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011972/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "c928e8b9515c5c0886aa5ec5b383c0b4",
22    "content_type": "seqspec",
23    "creation_timestamp": "2024-06-20T17:16:54.511503+00:00",
24    "file_format": "yaml",
25    "file_set": {
26        "@id": "/auxiliary-sets/IGVFDS4057PFBU/",
27        "@type": [
28            "AuxiliarySet",
29            "FileSet",
30            "Item"
31        ],
32        "accession": "IGVFDS4057PFBU",
33        "file_set_type": "gRNA sequencing",
34        "samples": [
35            {
36                "@id": "/in-vitro-systems/IGVFSM8511JOMW/",
37                "@type": [
38                    "InVitroSystem",
39                    "Biosample",
40                    "Sample",
41                    "Item"
42                ],
43                "accession": "IGVFSM8511JOMW",
44                "classifications": [
45                    "cell line"
46                ],
47                "modifications": [
48                    {
49                        "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
50                        "modality": "degradation",
51                        "status": "released",
52                        "summary": "AID system targeting RAD21"
53                    },
54                    {
55                        "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
56                        "modality": "interference",
57                        "status": "released",
58                        "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
59                    }
60                ],
61                "sample_terms": [
62                    {
63                        "@id": "/sample-terms/EFO_0002824/",
64                        "status": "released",
65                        "term_name": "HCT116"
66                    }
67                ],
68                "status": "released",
69                "summary": "Homo sapiens (male) HCT116 cell line treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library",
70                "taxa": "Homo sapiens",
71                "treatments": [
72                    {
73                        "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
74                        "purpose": "activation",
75                        "status": "released",
76                        "summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
77                        "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
78                    }
79                ]
80            }
81        ],
82        "status": "released",
83        "summary": "gRNA sequencing for mixed CRISPR TAP-seq integrating a guide (sgRNA) library targeting accessible genome regions in 29 genomic loci"
84    },
85    "file_size": 1172,
86    "gene_list_for": [],
87    "href": "/configuration-files/IGVFFI5301LVOU/@@download/IGVFFI5301LVOU.yaml.gz",
88    "input_file_for": [],
89    "integrated_in": [],
90    "lab": {
91        "@id": "/labs/jesse-engreitz/",
92        "title": "Jesse Engreitz, Stanford"
93    },
94    "loci_list_for": [],
95    "md5sum": "7fec665b48ba2ebf9eacb952c99e59ef",
96    "quality_metrics": [],
97    "release_timestamp": "2024-07-10T20:26:55.064149+00:00",
98    "s3_uri": "s3://igvf-files/2024/06/20/fe962ed8-b778-4568-91b6-c6bb0f0fb82f/IGVFFI5301LVOU.yaml.gz",
99    "schema_version": "7",
100    "seqspec_of": [
101        "/sequence-files/IGVFFI7212KPPW/",
102        "/sequence-files/IGVFFI7745NNEZ/",
103        "/sequence-files/IGVFFI8620YJXA/"
104    ],
105    "status": "released",
106    "submitted_by": {
107        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
108        "title": "Benjamin Doughty"
109    },
110    "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/240410_IGVF_upload/seqspec/tapseq_seqspec.out.Auxin6hrs-Rep2-S4.crispr.yaml.gz",
111    "summary": "seqspec of IGVFFI7212KPPW, IGVFFI7745NNEZ, IGVFFI8620YJXA",
112    "upload_status": "validation exempted",
113    "uuid": "fe962ed8-b778-4568-91b6-c6bb0f0fb82f",
114    "validate_onlist_files": false
115}