|
| Status |
Public on Jan 10, 2023 |
| Title |
Legacy_CRISPRi_V2_Plasmid_NextSeq |
| Sample type |
SRA |
| |
|
| Source name |
sample was not cloned into a cell
|
| Organism |
synthetic construct |
| Characteristics |
cell line: sample was not cloned into a cell
perturbation type: CRISPRi
crispr library: Addgene #83969
overall design: CRISPR guide RNA library cloning optimization
|
| Treatment protocol |
Dasatinib treatment samples (labeled as DASA) had a single dose of 0.75 nM of dasatinib was use as the drug selective pressure. Control samples (labeled as DMSO) were treated with 0.01% DMSO. Treatment was for 72 hours with 6 days of recovery.
|
| Growth protocol |
The K562 cultures were maintained at 500,000 cells / mL density for the duration of 7 days for the essential gene drop-out screens and 9 days for the dasatinib screens.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Macherey-Nagel Nucleospin Blood kits following the kit-specific protocols and quantified by Nanodrop.
Detailed protocol is in the supplemental materials. The main highlights are ordering insert oligo pools in both orientations, minimizing over amplification of the insert, and performing gel electrophoresis size selection and extraction at low temperatures.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Basecalls were performed using bclconvert or bcl2fastq. Count tables were generated using the ScreenProcessing pipeline.
Assembly: NCBI hg19
Supplementary files format and content: Text file with guide and and count
Library strategy: CRISPRi/a library sgRNA counts
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Jan 10, 2023 |
| Contact name |
Scot M Federman |
| E-mail(s) |
scot.federman@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Biochemistry
|
| Street address |
499 Illinois St
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL27609 |
| Series (1) |
| GSE222531 |
Optimized CRISPR guide RNA library cloning reduces skew and enables more compact genetic screens |
|
| Relations |
| BioSample |
SAMN32659282 |
| SRA |
SRX18989114 |
