IGVFFI8506ZTML

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI8506ZTML/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI8506ZTML",
10    "assay_titles": [
11        "lentiMPRA"
12    ],
13    "audit": {},
14    "award": {
15        "@id": "/awards/HG011966/",
16        "component": "functional characterization"
17    },
18    "content_md5sum": "24e76af14f6dcf6b62027b5242a2cd94",
19    "content_type": "reads",
20    "controlled_access": false,
21    "creation_timestamp": "2024-03-19T14:51:57.534323+00:00",
22    "externally_hosted": false,
23    "file_format": "fastq",
24    "file_set": {
25        "@id": "/measurement-sets/IGVFDS4302OZMS/",
26        "@type": [
27            "MeasurementSet",
28            "FileSet",
29            "Item"
30        ],
31        "accession": "IGVFDS4302OZMS",
32        "assay_term": {
33            "@id": "/assay-terms/OBI_0002675/",
34            "term_name": "massively parallel reporter assay"
35        },
36        "file_set_type": "experimental data",
37        "samples": [
38            {
39                "@id": "/in-vitro-systems/IGVFSM0720XHJA/",
40                "@type": [
41                    "InVitroSystem",
42                    "Biosample",
43                    "Sample",
44                    "Item"
45                ],
46                "accession": "IGVFSM0720XHJA",
47                "classifications": [
48                    "differentiated cell specimen",
49                    "pooled cell specimen"
50                ],
51                "sample_terms": [
52                    {
53                        "@id": "/sample-terms/EFO_0003042/",
54                        "status": "released",
55                        "term_name": "H1-hESC"
56                    }
57                ],
58                "status": "released",
59                "summary": "Homo sapiens (male) H1-hESC pooled differentiated cell specimen induced to glutamatergic neuron for 7 days transduced (lentivirus) with a reporter library",
60                "targeted_sample_term": {
61                    "@id": "/sample-terms/CL_0000679/",
62                    "status": "released",
63                    "term_name": "glutamatergic neuron"
64                },
65                "taxa": "Homo sapiens"
66            }
67        ],
68        "status": "released",
69        "summary": "lentiMPRA integrating a reporter library targeting histone modifications, transcription start sites, phenotype-associated variants genome-wide associated with autism spectrum disorder"
70    },
71    "file_size": 342814228,
72    "gene_list_for": [],
73    "href": "/sequence-files/IGVFFI8506ZTML/@@download/IGVFFI8506ZTML.fastq.gz",
74    "illumina_read_type": "R3",
75    "input_file_for": [
76        "/tabular-files/IGVFFI3167QVNF/",
77        "/tabular-files/IGVFFI7367TYXG/",
78        "/tabular-files/IGVFFI6886KJDH/",
79        "/tabular-files/IGVFFI0032GUOI/"
80    ],
81    "integrated_in": [],
82    "lab": {
83        "@id": "/labs/nadav-ahituv/",
84        "title": "Nadav Ahituv, UCSF"
85    },
86    "loci_list_for": [],
87    "maximum_read_length": 15,
88    "md5sum": "d9c09bf854e7d44ea44f338fa7b29267",
89    "mean_read_length": 15,
90    "minimum_read_length": 15,
91    "quality_metrics": [],
92    "read_count": 15744296,
93    "read_names": [
94        "Barcode reverse"
95    ],
96    "release_timestamp": "2025-01-09T20:34:27.236716+00:00",
97    "s3_uri": "s3://igvf-files/2024/03/19/4dae9a89-bc79-4ccd-94b4-ac77c0ecfd33/IGVFFI8506ZTML.fastq.gz",
98    "schema_version": "15",
99    "seqspecs": [
100        "/configuration-files/IGVFFI3444VJCS/"
101    ],
102    "sequencing_kit": "NextSeq 500 Mid Output v2 Kit",
103    "sequencing_platform": {
104        "@id": "/platform-terms/EFO_0009173/",
105        "status": "released",
106        "term_name": "Illumina NextSeq 500"
107    },
108    "sequencing_run": 1,
109    "status": "released",
110    "submitted_by": {
111        "@id": "/users/696ac72c-9846-469d-8bf1-8bd01856d4ba/",
112        "title": "Thorben Maass"
113    },
114    "submitted_file_name": "\"/data/cephfs-2/unmirrored/groups/kircher/IGVF_data_submssion_TM/ASD_nadav/counts/TSTFI48016273DNA_rep2_R3.fastq.gz\"",
115    "summary": "R3 reads from sequencing run 1",
116    "upload_status": "validated",
117    "uuid": "4dae9a89-bc79-4ccd-94b4-ac77c0ecfd33"
118}