IGVFFI6374XWBH

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI6374XWBH/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI6374XWBH",
10    "aliases": [
11        "jay-shendure:CRISPRa_singlecell_iPSCneuron_VPH_sequence_exprs_10Xlane2_seqlane1_R1"
12    ],
13    "assay_titles": [
14        "scCRISPR screen"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011966/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "e1ff29141718358c9f4e3bfefda0987a",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2023-12-09T00:51:42.953663+00:00",
25    "dbxrefs": [
26        "SRA:SRR30585986"
27    ],
28    "externally_hosted": false,
29    "file_format": "fastq",
30    "file_set": {
31        "@id": "/measurement-sets/IGVFDS0272VVTX/",
32        "@type": [
33            "MeasurementSet",
34            "FileSet",
35            "Item"
36        ],
37        "accession": "IGVFDS0272VVTX",
38        "assay_term": {
39            "@id": "/assay-terms/OBI_0003660/",
40            "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
41        },
42        "file_set_type": "experimental data",
43        "samples": [
44            {
45                "@id": "/in-vitro-systems/IGVFSM9913PXTT/",
46                "@type": [
47                    "InVitroSystem",
48                    "Biosample",
49                    "Sample",
50                    "Item"
51                ],
52                "accession": "IGVFSM9913PXTT",
53                "classifications": [
54                    "differentiated cell specimen"
55                ],
56                "modifications": [
57                    {
58                        "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
59                        "modality": "activation",
60                        "status": "released",
61                        "summary": "CRISPRa Sp-dCas9-VPH"
62                    }
63                ],
64                "sample_terms": [
65                    {
66                        "@id": "/sample-terms/EFO_0009747/",
67                        "status": "released",
68                        "term_name": "GM25256 (WTC-11)"
69                    }
70                ],
71                "status": "released",
72                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days (cellular sub pool: 10Xlane2) modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
73                "targeted_sample_term": {
74                    "@id": "/sample-terms/CL_0000540/",
75                    "status": "released",
76                    "term_name": "neuron"
77                },
78                "taxa": "Homo sapiens"
79            }
80        ],
81        "status": "released",
82        "summary": "scCRISPR activation screen integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
83    },
84    "file_size": 2104263570,
85    "flowcell_id": "AAAMCTVHV",
86    "gene_list_for": [],
87    "href": "/sequence-files/IGVFFI6374XWBH/@@download/IGVFFI6374XWBH.fastq.gz",
88    "illumina_read_type": "R1",
89    "input_file_for": [
90        "/matrix-files/IGVFFI8270PCLP/",
91        "/tabular-files/IGVFFI9048CVLI/",
92        "/tabular-files/IGVFFI4846IRZK/"
93    ],
94    "integrated_in": [],
95    "lab": {
96        "@id": "/labs/jay-shendure/",
97        "title": "Jay Shendure, UW"
98    },
99    "lane": 1,
100    "loci_list_for": [],
101    "maximum_read_length": 28,
102    "md5sum": "8c93ca7340eaa62ad7155b16f875b88b",
103    "mean_read_length": 28,
104    "minimum_read_length": 28,
105    "quality_metrics": [],
106    "read_count": 102168312,
107    "release_timestamp": "2024-08-13T20:47:22.363626+00:00",
108    "s3_uri": "s3://igvf-files/2023/12/09/fd5a8469-0aa3-467e-b17b-1acba11cbdcf/IGVFFI6374XWBH.fastq.gz",
109    "schema_version": "15",
110    "seqspecs": [
111        "/configuration-files/IGVFFI6477FWYH/"
112    ],
113    "sequencing_kit": "NextSeq 1000/2000 P3 Reagent Kit",
114    "sequencing_platform": {
115        "@id": "/platform-terms/EFO_0010963/",
116        "status": "released",
117        "term_name": "Illumina NextSeq 2000"
118    },
119    "sequencing_run": 1,
120    "status": "released",
121    "submitted_by": {
122        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
123        "title": "Beth Martin"
124    },
125    "submitted_file_name": "/net/shendure/vol10/www/content/members/CRISPRa_QTL_website/public/data/neuron_data/sequencing_data/cellranger_mkfastq_output/outs/fastq_path/AAAMCTVHV/exprs_2/exprs_2_S2_L001_R1_001.fastq.gz",
126    "summary": "R1 reads from sequencing run 1",
127    "upload_status": "validated",
128    "uuid": "fd5a8469-0aa3-467e-b17b-1acba11cbdcf"
129}