|
| Status |
Public on Jun 27, 2022 |
| Title |
Brunello_Input_S1_VSVG_Cre |
| Sample type |
SRA |
| |
|
| Source name |
Brunello plasmid DNA library
|
| Organism |
synthetic construct |
| Characteristics |
tissue: Brunello plasmid DNA library
cell line: Brunello plasmid DNA library
cell type: Brunello plasmid DNA library
genotype: Brunello plasmid DNA library
treatment: N/A
|
| Treatment protocol |
The cells were transduced with human CRISPR Brunello lentiviral pooled libraries and selected with Puromycin at 1ug/mL. Following selection, they were treated with different pseudoviruses for 48h. Then the cells were sorted in high and low GFP fluorescence in FACS.
|
| Growth protocol |
HEK293T cells were cultured in DMEM suppelemented with 10% FBS and 1% Penicillin/Streptomycin at 37C in 5% CO2 incubator.
|
| Extracted molecule |
other |
| Extraction protocol |
The genomic DNA was extracted from the sorted cells using Thermo scientific GeneJet Genomic DNA purification kit (Catalogue# K0721). Following extraction of genomic DNA, sgRNAs were amplified for seuqencing.
Equal molar amounts PCR gel-purified samples were pooled, denatured and diluted to 1.8pM, of which 1.3 ml was sequenced on a NextSeq 550 using a high output 75 cycle sequencing kit (Illumina)
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Sequencing reads were aligned to the Brunello library file and counted using MAGeCK 0.5.9.4.
Assembly: Brunello library
Supplementary files format and content: All the raw read count files from MAGeCK were combined into a single .txt file called “Count.files.txt”
Library strategy: CRISPR screen
|
| |
|
| Submission date |
Jun 27, 2022 |
| Last update date |
Jun 27, 2022 |
| Contact name |
Adam D. Hoppe |
| E-mail(s) |
adam.hoppe@sdstate.edu
|
| Phone |
6056955140
|
| Organization name |
South Dakota State University
|
| Department |
Chemistry and Biochemistry
|
| Lab |
Immunology
|
| Street address |
1055 CAMPANILE AVE BOX 2202, Avera Health and Science
|
| City |
Brookings |
| State/province |
South Dakota |
| ZIP/Postal code |
57007 |
| Country |
USA |
| |
|
| Platform ID |
GPL27609 |
| Series (1) |
| GSE206996 |
Differential Whole Genome CRISPR Screening Strategy for SARS-CoV-2 Spike and VSV-G Mediated Pseudoviral Entry |
|
| Relations |
| BioSample |
SAMN29369445 |
| SRA |
SRX15909387 |
