IGVFFI0779HVAM

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI0779HVAM/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI0779HVAM",
10    "aliases": [
11        "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin6hrs-FF2-BinA-PCR3_Rep2_S202"
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": "84b35e5e70774d7f80a5fc7853017931",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-06-01T02:07:50.456355+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS9717YXWE/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS9717YXWE",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0003661/",
37            "term_name": "in vitro CRISPR screen using flow cytometry"
38        },
39        "file_set_type": "experimental data",
40        "samples": [
41            {
42                "@id": "/in-vitro-systems/IGVFSM9689GGGO/",
43                "@type": [
44                    "InVitroSystem",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM9689GGGO",
50                "classifications": [
51                    "cell line"
52                ],
53                "modifications": [
54                    {
55                        "@id": "/degron-modifications/95081d1b-08b4-49ed-b324-e53fc43d8456/",
56                        "modality": "degradation",
57                        "status": "released",
58                        "summary": "AID system targeting RAD21"
59                    },
60                    {
61                        "@id": "/crispr-modifications/8543fa06-1720-4e7d-8e8f-7e24c1b1cf79/",
62                        "modality": "interference",
63                        "status": "released",
64                        "summary": "CRISPRi Sp-dCas9-KOX1-KRAB"
65                    }
66                ],
67                "sample_terms": [
68                    {
69                        "@id": "/sample-terms/EFO_0002824/",
70                        "status": "released",
71                        "term_name": "HCT116"
72                    }
73                ],
74                "status": "released",
75                "summary": "Homo sapiens (male) HCT116 cell line (sorting details: FACS bin A for 0-10% expression of MYC) 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",
76                "taxa": "Homo sapiens",
77                "treatments": [
78                    {
79                        "@id": "/treatments/d35868d1-c45b-49ae-8ff3-a9c0c22551c2/",
80                        "purpose": "activation",
81                        "status": "released",
82                        "summary": "Treatment of 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours",
83                        "treatment_term_name": "5-Phenyl-1H-indole-3-acetic acid"
84                    }
85                ]
86            }
87        ],
88        "status": "released",
89        "summary": "mixed CRISPR FlowFISH screen sorted on the expression of MYC integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
90    },
91    "file_size": 21148293,
92    "gene_list_for": [],
93    "href": "/sequence-files/IGVFFI0779HVAM/@@download/IGVFFI0779HVAM.fastq.gz",
94    "index": "AAGACACT:GCCA",
95    "input_file_for": [
96        "/tabular-files/IGVFFI3437ZDNT/"
97    ],
98    "integrated_in": [],
99    "lab": {
100        "@id": "/labs/jesse-engreitz/",
101        "title": "Jesse Engreitz, Stanford"
102    },
103    "loci_list_for": [],
104    "maximum_read_length": 21,
105    "md5sum": "fd8a0227626b3d380a1ca311a5b25736",
106    "mean_read_length": 21,
107    "minimum_read_length": 21,
108    "quality_metrics": [],
109    "read_count": 1073585,
110    "release_timestamp": "2024-07-10T20:21:32.756673+00:00",
111    "s3_uri": "s3://igvf-files/2024/06/01/81cbb67f-3e2c-4137-8d9d-00a634785141/IGVFFI0779HVAM.fastq.gz",
112    "schema_version": "15",
113    "seqspecs": [
114        "/configuration-files/IGVFFI6953RQCU/"
115    ],
116    "sequencing_platform": {
117        "@id": "/platform-terms/EFO_0008565/",
118        "status": "released",
119        "term_name": "Illumina HiSeq 2500"
120    },
121    "sequencing_run": 1,
122    "status": "released",
123    "submitted_by": {
124        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
125        "title": "Benjamin Doughty"
126    },
127    "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin6hrs-FF2-BinA-PCR3-Rep2_S202_R1_001.fastq.gz",
128    "summary": "reads from sequencing run 1",
129    "upload_status": "validated",
130    "uuid": "81cbb67f-3e2c-4137-8d9d-00a634785141"
131}