IGVFFI4454GSFQ

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI4454GSFQ/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI4454GSFQ",
10    "aliases": [
11        "charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep3-R1"
12    ],
13    "assay_titles": [
14        "CRISPR FACS screen"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012053/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "9a36ac8feeb8f74b446cf7eef996e793",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2023-11-08T20:31:07.525228+00:00",
25    "externally_hosted": false,
26    "file_format": "fastq",
27    "file_set": {
28        "@id": "/measurement-sets/IGVFDS6262JHMS/",
29        "@type": [
30            "MeasurementSet",
31            "FileSet",
32            "Item"
33        ],
34        "accession": "IGVFDS6262JHMS",
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": "/primary-cells/IGVFSM4110AXZO/",
43                "@type": [
44                    "PrimaryCell",
45                    "Biosample",
46                    "Sample",
47                    "Item"
48                ],
49                "accession": "IGVFSM4110AXZO",
50                "classifications": [
51                    "primary cell"
52                ],
53                "modifications": [
54                    {
55                        "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
56                        "modality": "activation",
57                        "status": "released",
58                        "summary": "CRISPRa Sa-dCas9-VP64"
59                    }
60                ],
61                "sample_terms": [
62                    {
63                        "@id": "/sample-terms/CL_0000909/",
64                        "status": "released",
65                        "term_name": "CD8-positive, alpha-beta memory T cell"
66                    }
67                ],
68                "status": "released",
69                "summary": "Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 0-10% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
70                "taxa": "Homo sapiens"
71            }
72        ],
73        "status": "released",
74        "summary": "low FACS signal CRISPR activation FACS screen sorted on the expression of CCR7 integrating a guide (sgRNA) library targeting transcription start sites in many genes"
75    },
76    "file_size": 53566286,
77    "flowcell_id": "000000000-K4RT4",
78    "gene_list_for": [],
79    "href": "/sequence-files/IGVFFI4454GSFQ/@@download/IGVFFI4454GSFQ.fastq.gz",
80    "illumina_read_type": "R1",
81    "input_file_for": [
82        "/alignment-files/IGVFFI5953CWOK/"
83    ],
84    "integrated_in": [],
85    "lab": {
86        "@id": "/labs/charles-gersbach/",
87        "title": "Charles Gersbach, Duke"
88    },
89    "lane": 1,
90    "loci_list_for": [],
91    "maximum_read_length": 22,
92    "md5sum": "c908c0c679fc55cd31df24d4eadd4714",
93    "mean_read_length": 22,
94    "minimum_read_length": 22,
95    "quality_metrics": [],
96    "read_count": 2296383,
97    "release_timestamp": "2024-11-18T21:08:52.732438+00:00",
98    "s3_uri": "s3://igvf-files/2023/11/08/3d68199e-0eb1-460a-b931-b7b28d594b76/IGVFFI4454GSFQ.fastq.gz",
99    "schema_version": "15",
100    "seqspecs": [],
101    "sequencing_kit": "MiSeq Reagent Kit v2",
102    "sequencing_platform": {
103        "@id": "/platform-terms/EFO_0004205/",
104        "status": "released",
105        "term_name": "Illumina MiSeq"
106    },
107    "sequencing_run": 3,
108    "status": "released",
109    "submitted_by": {
110        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
111        "title": "Alejandro Barrera"
112    },
113    "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/CCR7pos-pSM54-TF-L3_S9_L001_R1_001.fastq.gz",
114    "summary": "R1 reads from sequencing run 3",
115    "upload_status": "validated",
116    "uuid": "3d68199e-0eb1-460a-b931-b7b28d594b76"
117}