IGVFFI2664QRZC

released
validated
1{
2    "@context": "/terms/",
3    "@id": "/sequence-files/IGVFFI2664QRZC/",
4    "@type": [
5        "SequenceFile",
6        "File",
7        "Item"
8    ],
9    "accession": "IGVFFI2664QRZC",
10    "aliases": [
11        "charles-gersbach:hPA-Sequence-File-perturbseq-10xlane4-CRISPR-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": "f10b5b140abd3502ed8863c6f76ca908",
23    "content_type": "reads",
24    "controlled_access": false,
25    "creation_timestamp": "2025-04-09T21:04:39.469522+00:00",
26    "derived_manually": false,
27    "externally_hosted": false,
28    "file_format": "fastq",
29    "file_set": {
30        "@id": "/auxiliary-sets/IGVFDS7160FCCA/",
31        "@type": [
32            "AuxiliarySet",
33            "FileSet",
34            "Item"
35        ],
36        "accession": "IGVFDS7160FCCA",
37        "data_use_limitation_summaries": [
38            "no certificate"
39        ],
40        "file_set_type": "gRNA sequencing",
41        "samples": [
42            {
43                "@id": "/primary-cells/IGVFSM2166MHKA/",
44                "@type": [
45                    "PrimaryCell",
46                    "Biosample",
47                    "Sample",
48                    "Item"
49                ],
50                "accession": "IGVFSM2166MHKA",
51                "classifications": [
52                    "primary cell"
53                ],
54                "modifications": [
55                    {
56                        "@id": "/crispr-modifications/703c3934-6c9b-41d0-8481-e73cc64075f7/",
57                        "modality": "activation",
58                        "status": "released",
59                        "summary": "CRISPRa Sp-dCas9-2xVP64-2A-Puro"
60                    }
61                ],
62                "sample_terms": [
63                    {
64                        "@id": "/sample-terms/CL_0000127/",
65                        "status": "released",
66                        "term_name": "astrocyte"
67                    }
68                ],
69                "status": "released",
70                "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",
71                "taxa": "Homo sapiens",
72                "treatments": [
73                    {
74                        "@id": "/treatments/c7e73583-b639-473f-84c4-947cdc0bd81d/",
75                        "purpose": "differentiation",
76                        "status": "in progress",
77                        "summary": "Treatment of 20 ng/mL Brain-Derived Neurotrophic Factor",
78                        "treatment_term_name": "Brain-Derived Neurotrophic Factor"
79                    },
80                    {
81                        "@id": "/treatments/e23aab02-ae82-4935-85ad-1f238757f3ba/",
82                        "purpose": "differentiation",
83                        "status": "in progress",
84                        "summary": "Treatment of 10 ng/mL Neurotrophin-3",
85                        "treatment_term_name": "Neurotrophin-3"
86                    }
87                ]
88            }
89        ],
90        "status": "released",
91        "summary": "gRNA sequencing for CRISPR activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in many genes"
92    },
93    "file_size": 1340959267,
94    "gene_list_for": [],
95    "href": "/sequence-files/IGVFFI2664QRZC/@@download/IGVFFI2664QRZC.fastq.gz",
96    "illumina_read_type": "R2",
97    "input_file_for": [],
98    "integrated_in": [],
99    "lab": {
100        "@id": "/labs/charles-gersbach/",
101        "title": "Charles Gersbach, Duke"
102    },
103    "lane": 2,
104    "loci_list_for": [],
105    "maximum_read_length": 90,
106    "md5sum": "0effb6289b4a7ec63da13ca5f11af7b6",
107    "mean_read_length": 90,
108    "minimum_read_length": 90,
109    "quality_metrics": [],
110    "read_count": 44246590,
111    "read_names": [
112        "Read 2"
113    ],
114    "release_timestamp": "2025-05-16T16:07:13.012210+00:00",
115    "s3_uri": "s3://igvf-files/2025/04/09/fe45b1ae-7b8b-427f-915d-b8a6355b237e/IGVFFI2664QRZC.fastq.gz",
116    "schema_version": "16",
117    "seqspecs": [
118        "/configuration-files/IGVFFI3935RVGM/"
119    ],
120    "sequencing_kit": "NovaSeq 6000 S2 Reagent Kit v1.5",
121    "sequencing_platform": {
122        "@id": "/platform-terms/EFO_0008637/",
123        "status": "released",
124        "term_name": "Illumina NovaSeq 6000"
125    },
126    "sequencing_run": 4,
127    "status": "released",
128    "submitted_by": {
129        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
130        "title": "Ruhi Rai"
131    },
132    "submitted_file_name": "/work/rr151/SamAIM2neuro_data/CRISPR_4_S4_L002_R2_001.fastq.gz",
133    "summary": "R2 reads from sequencing run 4",
134    "upload_status": "validated",
135    "uuid": "fe45b1ae-7b8b-427f-915d-b8a6355b237e"
136}