IGVFFI1223MSKP

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI1223MSKP/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI1223MSKP",
10    "aliases": [
11        "jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep1-BinB-PCRrep5_I1"
12    ],
13    "assay_titles": [
14        "Variant-EFFECTS"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011972/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "399661ced0358e82432cfefc10408bb4",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2023-12-13T15:05:38.556530+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS4916MNSK/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS4916MNSK",
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/IGVFSM0519CRES/",
43                "@type": [
44                    "InVitroSystem",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM0519CRES",
50                "classifications": [
51                    "cell line"
52                ],
53                "modifications": [
54                    {
55                        "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
56                        "modality": "prime editing",
57                        "status": "released",
58                        "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
59                    }
60                ],
61                "sample_terms": [
62                    {
63                        "@id": "/sample-terms/EFO_0002796/",
64                        "status": "released",
65                        "term_name": "Jurkat"
66                    }
67                ],
68                "status": "released",
69                "summary": "Homo sapiens (male) Jurkat 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",
70                "taxa": "Homo sapiens"
71            }
72        ],
73        "status": "released",
74        "summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
75    },
76    "file_size": 1923470,
77    "gene_list_for": [],
78    "href": "/sequence-files/IGVFFI1223MSKP/@@download/IGVFFI1223MSKP.fastq.gz",
79    "illumina_read_type": "I1",
80    "index": "GTCTGATG:CAGT",
81    "input_file_for": [
82        "/tabular-files/IGVFFI8402CAPM/"
83    ],
84    "integrated_in": [],
85    "lab": {
86        "@id": "/labs/jesse-engreitz/",
87        "title": "Jesse Engreitz, Stanford"
88    },
89    "loci_list_for": [],
90    "maximum_read_length": 8,
91    "md5sum": "8e26ba8b00d8b60bb9438ea6e9a97e84",
92    "mean_read_length": 8,
93    "minimum_read_length": 8,
94    "quality_metrics": [],
95    "read_count": 238847,
96    "release_timestamp": "2023-12-21T01:01:56.749141+00:00",
97    "s3_uri": "s3://igvf-files/2023/12/13/fd795002-ed71-429d-b820-ad73583103b2/IGVFFI1223MSKP.fastq.gz",
98    "schema_version": "15",
99    "seqspecs": [],
100    "sequencing_platform": {
101        "@id": "/platform-terms/EFO_0008566/",
102        "status": "released",
103        "term_name": "Illumina NextSeq 550"
104    },
105    "sequencing_run": 1,
106    "status": "released",
107    "submitted_by": {
108        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
109        "title": "Michael Montgomery"
110    },
111    "submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep1_BinB-PCRrep5_S17_I1_001.fastq.gz",
112    "summary": "I1 reads from sequencing run 1",
113    "upload_status": "validated",
114    "uuid": "fd795002-ed71-429d-b820-ad73583103b2"
115}