|
Status |
Public on Dec 15, 2020 |
Title |
T. gondii- WT treated 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: 5uM sodium arsenite
|
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 |
SAMN16213006 |
SRA |
SRX9152693 |