IGVFFI4334TLKF

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4334TLKF/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4334TLKF",
10    "aliases": [
11        "jesse-engreitz:auxiliary_file_CRUDO_MYC-Auxin0hrs-FF2-BinE-PCR1_Rep1_S29"
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": "dfb1790f7d8794de5a11ffb924fa74fe",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-06-01T02:00:58.432177+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS5847JIJX/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS5847JIJX",
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/IGVFSM1124JJAA/",
43                "@type": [
44                    "InVitroSystem",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM1124JJAA",
50                "classifications": [
51                    "cell line"
52                ],
53                "modifications": [
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                        "@id": "/degron-modifications/2e8d10cc-fc98-44d5-a7d9-e2892e16c98a/",
62                        "modality": "degradation",
63                        "status": "released",
64                        "summary": "inactive AID system targeting RAD21"
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 E for 80-90% expression of MYC) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library",
76                "taxa": "Homo sapiens"
77            }
78        ],
79        "status": "released",
80        "summary": "mixed CRISPR FlowFISH screen sorted on the expression of MYC integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci"
81    },
82    "file_size": 36825085,
83    "gene_list_for": [],
84    "href": "/sequence-files/IGVFFI4334TLKF/@@download/IGVFFI4334TLKF.fastq.gz",
85    "index": "TCGCCTTG:TGCG",
86    "input_file_for": [
87        "/tabular-files/IGVFFI3437ZDNT/"
88    ],
89    "integrated_in": [],
90    "lab": {
91        "@id": "/labs/jesse-engreitz/",
92        "title": "Jesse Engreitz, Stanford"
93    },
94    "loci_list_for": [],
95    "maximum_read_length": 21,
96    "md5sum": "a7d6c0d639f9afa1c2b737f35d2969f3",
97    "mean_read_length": 21,
98    "minimum_read_length": 21,
99    "quality_metrics": [],
100    "read_count": 1887479,
101    "release_timestamp": "2024-07-10T20:20:31.339610+00:00",
102    "s3_uri": "s3://igvf-files/2024/06/01/a7d23454-e9c5-4732-994f-9aa05969c03a/IGVFFI4334TLKF.fastq.gz",
103    "schema_version": "15",
104    "seqspecs": [
105        "/configuration-files/IGVFFI1277NHCZ/"
106    ],
107    "sequencing_platform": {
108        "@id": "/platform-terms/EFO_0008565/",
109        "status": "released",
110        "term_name": "Illumina HiSeq 2500"
111    },
112    "sequencing_run": 1,
113    "status": "released",
114    "submitted_by": {
115        "@id": "/users/100f06c6-83a7-4b4d-9dfd-053a1829773b/",
116        "title": "Benjamin Doughty"
117    },
118    "submitted_file_name": "/oak/stanford/groups/engreitz/Projects/Cohesin/220819B015_MYC/fastq_trim/MYC-Auxin0hrs-FF2-BinE-PCR1-Rep1_S29_R1_001.fastq.gz",
119    "summary": "reads from sequencing run 1",
120    "upload_status": "validated",
121    "uuid": "a7d23454-e9c5-4732-994f-9aa05969c03a"
122}