IGVFFI3023HOII

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI3023HOII/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI3023HOII",
10    "aliases": [
11        "charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-GEX-L2-R2"
12    ],
13    "assay_titles": [
14        "Perturb-seq"
15    ],
16    "audit": {},
17    "award": {
18        "@id": "/awards/HG012053/",
19        "component": "functional characterization"
20    },
21    "checkfiles_version": "v20",
22    "content_md5sum": "4d836b750ccac96ac1f45ee110544d80",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-04-09T21:04:08.146597+00:00",
26    "derived_manually": false,
27    "externally_hosted": false,
28    "file_format": "fastq",
29    "file_set": {
30        "@id": "/measurement-sets/IGVFDS4521RIQF/",
31        "@type": [
32            "MeasurementSet",
33            "FileSet",
34            "Item"
35        ],
36        "accession": "IGVFDS4521RIQF",
37        "assay_term": {
38            "@id": "/assay-terms/OBI_0003660/",
39            "term_name": "in vitro CRISPR screen using single-cell RNA-seq"
40        },
41        "data_use_limitation_summaries": [
42            "no certificate"
43        ],
44        "file_set_type": "experimental data",
45        "samples": [
46            {
47                "@id": "/primary-cells/IGVFSM2166MHKA/",
48                "@type": [
49                    "PrimaryCell",
50                    "Biosample",
51                    "Sample",
52                    "Item"
53                ],
54                "accession": "IGVFSM2166MHKA",
55                "classifications": [
56                    "primary cell"
57                ],
58                "modifications": [
59                    {
60                        "@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
61                        "modality": "activation",
62                        "status": "released",
63                        "summary": "CRISPRa Sp-dCas9-2xVP64-2A-Puro"
64                    }
65                ],
66                "sample_terms": [
67                    {
68                        "@id": "/sample-terms/CL_0000127/",
69                        "status": "released",
70                        "term_name": "astrocyte"
71                    }
72                ],
73                "status": "released",
74                "summary": "Homo sapiens astrocyte cell treated with 10 ng/mL Neurotrophin-3, 20 ng/mL Brain-Derived Neurotrophic Factor, modified with CRISPRa Sp-dCas9-2xVP64-2A-Puro, transduced (lentivirus) with a guide library",
75                "taxa": "Homo sapiens",
76                "treatments": [
77                    {
78                        "@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
79                        "purpose": "differentiation",
80                        "status": "in progress",
81                        "summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
82                        "treatment_term_name": "Brain-Derived Neurotrophic Factor"
83                    },
84                    {
85                        "@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
86                        "purpose": "differentiation",
87                        "status": "in progress",
88                        "summary": "Treatment of 10 ng/mL Neurotrophin-3",
89                        "treatment_term_name": "Neurotrophin-3"
90                    }
91                ]
92            }
93        ],
94        "status": "released",
95        "summary": "CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes"
96    },
97    "file_size": 9263790502,
98    "gene_list_for": [],
99    "href": "/sequence-files/IGVFFI3023HOII/@@download/IGVFFI3023HOII.fastq.gz",
100    "illumina_read_type": "R2",
101    "input_file_for": [],
102    "integrated_in": [],
103    "lab": {
104        "@id": "/labs/charles-gersbach/",
105        "title": "Charles Gersbach, Duke"
106    },
107    "lane": 2,
108    "loci_list_for": [],
109    "maximum_read_length": 90,
110    "md5sum": "c02eced43c21f2cde40d6ace9bb1e2d1",
111    "mean_read_length": 90,
112    "minimum_read_length": 90,
113    "quality_metrics": [],
114    "read_count": 183912212,
115    "read_names": [
116        "Read 2"
117    ],
118    "release_timestamp": "2025-05-16T16:07:13.060756+00:00",
119    "s3_uri": "s3://igvf-files/2025/04/09/85fb475e-0be7-4f73-bc8a-351ef2c01986/IGVFFI3023HOII.fastq.gz",
120    "schema_version": "16",
121    "seqspecs": [
122        "/configuration-files/IGVFFI4747OOCN/"
123    ],
124    "sequencing_kit": "NovaSeq 6000 S2 Reagent Kit v1.5",
125    "sequencing_platform": {
126        "@id": "/platform-terms/EFO_0008637/",
127        "status": "released",
128        "term_name": "Illumina NovaSeq 6000"
129    },
130    "sequencing_run": 4,
131    "status": "released",
132    "submitted_by": {
133        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
134        "title": "Ruhi Rai"
135    },
136    "submitted_file_name": "/work/rr151/SamAIM2neuro_data/GEX_4_S4_L002_R2_001.fastq.gz",
137    "summary": "R2 reads from sequencing run 4",
138    "upload_status": "validated",
139    "uuid": "85fb475e-0be7-4f73-bc8a-351ef2c01986"
140}