|
| Status |
Public on Jul 17, 2017 |
| Title |
Sequencing of the transduced sgRNAs post-selection (Screen B)_lane 2 |
| Sample type |
SRA |
| |
|
| Source name |
A549 Cells
|
| Organism |
Mus musculus |
| Characteristics |
sample type: transduced sgRNAs post-selection (Screen B)
|
| Treatment protocol |
Cells were transduced with sgRNA lentivirus and subsequently infected with influenza A virus (PR8 strain).
|
| Growth protocol |
Cells were grown under standard laboratory conditions and stably transfected with CRISPR components.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were sorted via flow cytometry, genomic DNA was extracted, and PCR for the sgRNA sequences was performed.
Illumina adaptors and barcodes were incorporated into the PCR primers.
PCR amplified libraries were generated with independent barcodes to allow multiplexing. 50% PhiX DNA was included in the sequencing run, as low diversity libraries were expected.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Double Lane Sequencing
HiSeq2000 Rapid Run
Neg B NH
|
| Data processing |
The sgRNA reads (which had 5' and 3' flanking regions that matched the sgRNA expression lentivirus vector) were quality filtered and mapped to a reference table of sgRNA sequences provided in Konermann et al, Nature 2015 (supplementary table 6).
Read numbers were normalized by dividing by the total read depth to give a percentage of total reads (displayed in the "percentage of reads" column in the processed data tables).
Supplementary_files_format_and_content: Raw and normalized read numbers
|
| |
|
| Submission date |
Nov 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas Heaton |
| E-mail(s) |
nicholas.heaton@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Molecular Genetics and Microbiology
|
| Street address |
213 Research Drive, 426 CARL Building
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27710 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE89371 |
A genome-wide CRISPR activation screen identifies B4GALNT2 as an inhibitory host factor for influenza virus infection |
|
| Relations |
| BioSample |
SAMN05958564 |
| SRA |
SRX2312505 |
