|
| Status |
Public on Mar 26, 2024 |
| Title |
ME49_IAA-24h_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
ME49-TIR1 eIF4E1mAID-HA
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell line: ME49-TIR1 eIF4E1mAID-HA
treatment: 500uM IAA, 24h
|
| Treatment protocol |
treatment with 500 uM 3-indole acetic acid (IAA) for 24h or 48h
|
| Growth protocol |
parasites innoculated at MOI 2:1, grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 16h prior to addition of 0.5% DMSO (vehicle) or 500uM IAA
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
infected monolayer was scraped & syringe lysed. Parasites washed once with PBS. Pellet resuspended in TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
paired end 2x150bp RNAseq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
map fastq with hisat2 using default settings
count reads with htseq-count
differential gene expression with DESeq2
Assembly: ME49 genome v54, available at toxodb.org
Supplementary files format and content: tab delimited file with gene counts
|
| |
|
| Submission date |
Mar 22, 2024 |
| Last update date |
Mar 26, 2024 |
| Contact name |
Michael James Holmes |
| E-mail(s) |
[email protected]
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Pharmacology & Toxicology
|
| Street address |
635 Barnhill Drive
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL26742 |
| Series (1) |
| GSE262241 |
Timecourse of transcriptional changes upon eIF4E1 depletion in Toxoplasma gondii |
|
| Relations |
| BioSample |
SAMN40582155 |
| SRA |
SRX24025861 |
