|
| Status |
Public on Feb 28, 2018 |
| Title |
Rd2_selection_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
A549-GeCKO_Rd2_selection
|
| Organism |
Homo sapiens |
| Characteristics |
cell line background: A549
cell type: Human lung epithelial cells
genotype/variation: A549-GeCKO; pooled library of A549 cells lacking individual gene
subjected to: multiple rounds of lethal influenza virus infection (H5N1 low pathogenic) -Round 2 (Replicate 1)
|
| Treatment protocol |
A549 cells were transduced with sgRNA lentivirus and infected with low pathogenic H5N1 virus
|
| Growth protocol |
A549 cells were cultured in standard conditions: passaged every 48hr in DMEM containing 10% fetal bovine serum and 1% penicilin/streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using the Blood and Cell Culture Maxi Kit or Mini Kit (Qiagen)
Genomic DNA from naïve cells or cells surviving lethal H5N1 infection was extracted. The integrated sgRNA cassette was PCR amplified from genomic DNA. Illumina barcodes were incorporated in the PCR primers.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
BM-13_S13
|
| Data processing |
The occurrence of sgRNAs indexes were summarized with the Bioconductor Biostrings package (PDict class)
Enriched genes were identified via MAGeCK, a Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout method for prioritizing single-guide RNAs, genes, and pathways in genome-scale CRISPR/Cas9 knockout screens
Genome_build: Human GeCKO v2 half-library A (can be used in either 1- or 2-plasmid systems)
Supplementary_files_format_and_content: tab-delimited text files, csv and excel files include the occurrence of each sgRNA indexes in Library A for each sample separately
|
| |
|
| Submission date |
Feb 27, 2018 |
| Last update date |
Feb 28, 2018 |
| Contact name |
Yan Li |
| E-mail(s) |
yli22@bsd.uchicago.edu
|
| Phone |
7738344316
|
| Organization name |
The University of Chicago
|
| Department |
Center for Research Informatics
|
| Street address |
900 East 57th St.
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE111166 |
Genome-Wide CRISPR/Cas9 Screen Identifies Host Factors Essential for Influenza Virus Replication |
|
| Relations |
| BioSample |
SAMN08613584 |
| SRA |
SRX3745266 |
