IGVFFI4019NMPR

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4019NMPR/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4019NMPR",
10    "aliases": [
11        "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB-PCRrep9_I2"
12    ],
13    "assay_titles": [
14        "Variant-EFFECTS"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011972/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "d30930e6bc711d36d04ca7ae863c53db",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2023-12-05T22:36:44.417595+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS5601DSMT/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS5601DSMT",
35        "assay_term": {
36            "@id": "/assay-terms/OBI_0003661/",
37            "term_name": "in vitro CRISPR screen using flow cytometry"
38        },
39        "data_use_limitation_summaries": [
40            "no certificate"
41        ],
42        "file_set_type": "experimental data",
43        "samples": [
44            {
45                "@id": "/in-vitro-systems/IGVFSM1683OFWB/",
46                "@type": [
47                    "InVitroSystem",
48                    "Biosample",
49                    "Sample",
50                    "Item"
51                ],
52                "accession": "IGVFSM1683OFWB",
53                "classifications": [
54                    "cell line"
55                ],
56                "modifications": [
57                    {
58                        "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
59                        "modality": "prime editing",
60                        "status": "released",
61                        "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
62                    }
63                ],
64                "sample_terms": [
65                    {
66                        "@id": "/sample-terms/EFO_0001253/",
67                        "status": "released",
68                        "term_name": "THP-1"
69                    }
70                ],
71                "status": "released",
72                "summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
73                "taxa": "Homo sapiens"
74            }
75        ],
76        "status": "released",
77        "summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
78    },
79    "file_size": 829658,
80    "gene_list_for": [],
81    "href": "/sequence-files/IGVFFI4019NMPR/@@download/IGVFFI4019NMPR.fastq.gz",
82    "illumina_read_type": "I2",
83    "index": "ATTATGTT:TGAC",
84    "input_file_for": [
85        "/tabular-files/IGVFFI0647QQKM/"
86    ],
87    "integrated_in": [],
88    "lab": {
89        "@id": "/labs/jesse-engreitz/",
90        "title": "Jesse Engreitz, Stanford"
91    },
92    "loci_list_for": [],
93    "maximum_read_length": 4,
94    "md5sum": "7a56744e9ffd4ebbee2d0e3af13d7289",
95    "mean_read_length": 4,
96    "minimum_read_length": 4,
97    "quality_metrics": [],
98    "read_count": 97009,
99    "release_timestamp": "2023-12-20T23:49:26.213233+00:00",
100    "s3_uri": "s3://igvf-files/2023/12/05/bca35b1c-a779-48a1-932a-894aad32a210/IGVFFI4019NMPR.fastq.gz",
101    "schema_version": "15",
102    "seqspecs": [],
103    "sequencing_platform": {
104        "@id": "/platform-terms/EFO_0008566/",
105        "status": "released",
106        "term_name": "Illumina NextSeq 550"
107    },
108    "sequencing_run": 1,
109    "status": "released",
110    "submitted_by": {
111        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
112        "title": "Michael Montgomery"
113    },
114    "submitted_file_name": "230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB-PCRrep9_S351_I2_001.fastq.gz",
115    "summary": "I2 reads from sequencing run 1",
116    "upload_status": "validated",
117    "uuid": "bca35b1c-a779-48a1-932a-894aad32a210"
118}