IGVFFI9417VJMJ

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI9417VJMJ/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI9417VJMJ",
10    "aliases": [
11        "jay-shendure:CRISPRa_singlevalidations_neurons_TCF4_rep2_R2"
12    ],
13    "assay_titles": [
14        "RNA-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG011966/",
19        "component": "functional characterization"
20    },
21    "content_md5sum": "95d04f637903ca2da89b9de15d07f694",
22    "content_type": "reads",
23    "controlled_access": false,
24    "creation_timestamp": "2024-10-18T16:36:55.485909+00:00",
25    "derived_manually": false,
26    "externally_hosted": false,
27    "file_format": "fastq",
28    "file_set": {
29        "@id": "/measurement-sets/IGVFDS4796HVFQ/",
30        "@type": [
31            "MeasurementSet",
32            "FileSet",
33            "Item"
34        ],
35        "accession": "IGVFDS4796HVFQ",
36        "assay_term": {
37            "@id": "/assay-terms/OBI_0003090/",
38            "term_name": "bulk RNA-seq assay"
39        },
40        "controlled_access": false,
41        "data_use_limitation_summaries": [
42            "No limitations"
43        ],
44        "file_set_type": "experimental data",
45        "samples": [
46            {
47                "@id": "/in-vitro-systems/IGVFSM1303ELWI/",
48                "@type": [
49                    "InVitroSystem",
50                    "Biosample",
51                    "Sample",
52                    "Item"
53                ],
54                "accession": "IGVFSM1303ELWI",
55                "classifications": [
56                    "differentiated cell specimen"
57                ],
58                "modifications": [
59                    {
60                        "@id": "/crispr-modifications/426a4099-35d9-4c65-8851-5e788a3d4e70/",
61                        "modality": "activation",
62                        "status": "released",
63                        "summary": "CRISPRa Sp-dCas9-VPH"
64                    }
65                ],
66                "sample_terms": [
67                    {
68                        "@id": "/sample-terms/EFO_0009747/",
69                        "status": "released",
70                        "term_name": "GM25256 (WTC-11)"
71                    }
72                ],
73                "status": "released",
74                "summary": "Homo sapiens (male) GM25256 (WTC-11) differentiated cell specimen induced to neuron for 19 days modified with CRISPRa Sp-dCas9-VPH, transfected with a guide library",
75                "targeted_sample_term": {
76                    "@id": "/sample-terms/CL_0000540/",
77                    "status": "released",
78                    "term_name": "neuron"
79                },
80                "taxa": "Homo sapiens"
81            }
82        ],
83        "status": "released",
84        "summary": "CRISPR activation RNA-seq integrating a guide (sgRNA) library targeting TF binding sites, candidate cis-regulatory elements in many genomic loci"
85    },
86    "file_size": 292048028,
87    "gene_list_for": [],
88    "href": "/sequence-files/IGVFFI9417VJMJ/@@download/IGVFFI9417VJMJ.fastq.gz",
89    "input_file_for": [
90        "/tabular-files/IGVFFI0765KKLP/"
91    ],
92    "integrated_in": [],
93    "lab": {
94        "@id": "/labs/jay-shendure/",
95        "title": "Jay Shendure, UW"
96    },
97    "lane": 1,
98    "loci_list_for": [],
99    "maximum_read_length": 110,
100    "md5sum": "7cffa06f8d09a47f5145523d9548015f",
101    "mean_read_length": 110,
102    "minimum_read_length": 110,
103    "quality_metrics": [],
104    "read_count": 5341472,
105    "release_timestamp": "2025-05-29T21:02:02.729683+00:00",
106    "s3_uri": "s3://igvf-files/2024/10/18/fa3cb17d-410c-4c9d-b9a6-e291ee52d77c/IGVFFI9417VJMJ.fastq.gz",
107    "schema_version": "16",
108    "seqspecs": [
109        "/configuration-files/IGVFFI6870AJBX/"
110    ],
111    "sequencing_kit": "NextSeq 1000/2000 P1 Reagent Kit",
112    "sequencing_platform": {
113        "@id": "/platform-terms/EFO_0010963/",
114        "status": "released",
115        "term_name": "Illumina NextSeq 2000"
116    },
117    "sequencing_run": 1,
118    "status": "released",
119    "submitted_by": {
120        "@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
121        "title": "Beth Martin"
122    },
123    "submitted_file_name": "/net/shendure/vol10/projects/IGVFtemp/pooled_fastqs/Neuron_gRNA_21_Rep_2_TCF4_S23_R2_001.fastq.gz",
124    "summary": "reads from sequencing run 1",
125    "upload_status": "validated",
126    "uuid": "fa3cb17d-410c-4c9d-b9a6-e291ee52d77c"
127}