|
| Status |
Public on Apr 16, 2019 |
| Title |
GeCKO screen for DENV-4 using Huh7.5.1 cells |
| Sample type |
SRA |
| |
|
| Source name |
Dengue virus infection
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Huh7.5.1
cell type: Hepatocarcinoma cell line
gender: male
|
| Treatment protocol |
Cells were mutagenized using GeCKO V2 libraries (PMID:25075903)
|
| Growth protocol |
Huh7.5.1 cells were grown in DMEM with 10% FBS and 1% penicillin-streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Virus resistant cells were harvested for total genomic DNA extraction using QIAamp DNA Mini Kit (Qiagen)
Libraries were prepared as previously reported (PMID: 27383987)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CRISPR/Cas9 mutated genomic DNA
|
| Data processing |
Library strategy: Genome Scale CRISPR KO (GeCKO, V2)
Sequencing reads were analyzed using MAGeCK algorithm, taking into account multiple different sgRNAs per gene, number of sequencing reads per gene, and the enrichment of sgRNAs compared to the uninfected pooled library (PMID: 25476604)
Each screen data was individually analyzed, and combined as 4 replicates for MAGeCK analysis
|
| |
|
| Submission date |
Jan 15, 2018 |
| Last update date |
Apr 16, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE109192 |
An RNA-centric dissection of host complexes controlling flavivirus infection [GeCKO] |
| GSE109194 |
An RNA-centric dissection of host complexes controlling flavivirus infection |
|
| Relations |
| BioSample |
SAMN08365469 |
| SRA |
SRX3584811 |
