|
| Status |
Public on Dec 15, 2020 |
| Title |
T. gondii- WT untreated 3 |
| Sample type |
SRA |
| |
|
| Source name |
intracellular T. gondii
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell type: Toxoplasma gondii- tachyzoite
strain: ME49
host cell: Human Foreskin Fibroblast
genotype: wild-type
treatment: untreated
|
| Treatment protocol |
Purified parasites were washed in DMEM and centrifuge 300g for 15 min. Purified extracellular WT and Δtgif2k-b tachyzoites were treated with vehicle or 5 µM sodium arsenite for 2 h at 37°C
|
| Growth protocol |
Tachyzoites were allowed to invade HFF host cell monolayers for 2 h, then infected monolayers were washed and replaced with fresh medium. At 36 hours post-infection, intracellular tachyzoites were harvested from HFFs by syringe passage and filtering
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen Rneasy kit
Library construction and sequencing was performed by Genewiz
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The quality of the raw sequencing reads obtained from GENEWIZ was checked using FastQC (PMID: 30254741) and the low-quality reads were trimmed using TrimGalore (PMID: 22748135).
Trimmed reads were aligned to the reference T. gondii ME49 genome (ToxoDB.org) using hierarchical indexing for spliced alignment of transcripts (HISAT2) (PMID: 25751142).
The number of reads aligning to the exons of different genes were counted using featureCounts (PMID: 24227677).
Differential experession analysis was perfomed using DESeq2
Genome_build: ME49- ToxoDB.org
Supplementary_files_format_and_content: feature counts in tab delimited text format
|
| |
|
| Submission date |
Sep 18, 2020 |
| Last update date |
Dec 20, 2020 |
| Contact name |
Ronald C Wek |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
635 N. Barnhill Dr. MS4067
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL23466 |
| Series (1) |
| GSE158231 |
TgIF2K-B is an eIF2α kinase in Toxoplasma gondii that responds to oxidative stress and optimizes pathogenicity |
|
| Relations |
| BioSample |
SAMN16213013 |
| SRA |
SRX9152690 |
