|
| Status |
Public on Jul 20, 2017 |
| Title |
Croatan_dual_screen_K562_T0_R3 |
| Sample type |
SRA |
| |
|
| Source name |
K562-Cas9 cells
|
| Organism |
synthetic construct |
| Characteristics |
timepoint: T0
library: Croatan dual sgRNA screen library
|
| Treatment protocol |
Cells were infected with lentivirus harboring sgRNA libraries, with an MOI of 0.3, and were kept in culture for 12 doublings
|
| Growth protocol |
A375 and K562 cell lines were grown at 37C with 5% CO2 according to ATCC guidelines
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted 2 days after infection (T0) and after 12 doublings (T6) using the QIAamp Blood DNA Midi Kit (Qiagen).
For each sample, sgRNA sequences were extracted from genomic DNA in 8 separate 30-cycle PCR reactions where 2 ug of input DNA was included in each reaction. Illumina adapters where included on the PCR primers for this PCR.
Samples were sequenced on the Illumina MiSeq platform.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Croatan_dual_screen_counts.txt
|
| Data processing |
Trim reads to 20bp using fastx_trimmer (-l20) (FASTX Toolkit 0.0.13.2)
Map reads to relevant sgRNA index using bowtie v1.1.0 (options: -v0 --norc)
Count total mapped reads per sgRNA using awk
Join total counts from samples for each library and cell line using join
Supplementary_files_format_and_content: Counts of sgRNAs for different timepoints
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolas Erard |
| E-mail(s) |
[email protected]
|
| Organization name |
CRUK Cambridge Institute
|
| Lab |
Hannon Lab
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17769 |
| Series (2) |
| GSE97432 |
An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout II |
| GSE97434 |
An arrayed CRISPR library for individual, combinatorial and multiplexed gene knockout |
|
| Relations |
| BioSample |
SAMN06688902 |
| SRA |
SRX2711083 |
