|
| Status |
Public on Jul 04, 2020 |
| Title |
Rep3_DHA_0.5_uM |
| Sample type |
SRA |
| |
|
| Source name |
SgRNAs from a pool of T gondii mutants generated using CRISPR, then treated with 0.5 uM DHA
|
| Organism |
Toxoplasma gondii |
| Characteristics |
replicate: 3
treatment: 0.5 uM DHA
|
| Treatment protocol |
Cas9-expressing parasites were transfected with sgRNA-expressing plasmids, cultured for approximately one week (until passage 3, or P3) then cultured with DHA or vehicle control for a approximately one additional week.
|
| Growth protocol |
See PMID 27594426, 29323662 and BioRxiv https://doi.org/10.1101/746974
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from parasites using a Dneasy DNA extraction kit from Qiagen and sgRNAs were amplified using custom primers (see PMID 29323662).
See PMID 29323662
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
sgRNAs were counted using a custom analysis script (see PMID 29323662).
Supplementary_files_format_and_content: The file allDHAcounts.csv contains the processed data for all the fastq files. Each column in allDHAcounts.csv was generated by counting the sgRNAs for each gene in a particular fastq file.
|
| |
|
| Submission date |
Jul 03, 2020 |
| Last update date |
Jul 04, 2020 |
| Contact name |
Sebastian Lourido |
| E-mail(s) |
lourido@wi.mit.edu
|
| Organization name |
Whitehead Institute
|
| Lab |
Lourido Lab
|
| Street address |
455 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL16774 |
| Series (1) |
| GSE153785 |
Genome-Wide CRISPR Screens for Toxoplasma Gondii Genes Related to Artemisinin Susceptibility |
|
| Relations |
| BioSample |
SAMN15445630 |
| SRA |
SRX8665403 |
