|
| Status |
Public on Nov 02, 2023 |
| Title |
eIF4E1_IAA_RNAseq_2 |
| Sample type |
SRA |
| |
|
| Source name |
RH::TIR1 parental strain
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell line: RH::TIR1 parental strain
cell type: tachyzoites
|
| Treatment protocol |
treatment with 0.5% DMSO vehicle or 500uM indole-3-acetic acid (IAA) for 4 hours prior to harvest.
|
| Growth protocol |
parasites innoculated and grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 48h prior to harvest
|
| Extracted molecule |
cytoplasmic RNA |
| Extraction protocol |
cytoplasmic lysate was collected and an aliquot was immediately stored in Trizol for RNA-seq samples. The rest was digested with RNaseI and monosomes were collecte by ultracentrifugation on a sucrose gradient. Ribosome-protected fragments (RFP) were purified after gel electrophoresis
total RNA was fragmented by alkaline hydrolysis. Fragments were purfied by gel electrophoresis. fragments were dephosphorylated, ligated at 5' end with barcoded adapter, rRNA removal with sequential treatment of sample with riboPOOLs kit for human then Toxoplasma, phosphorylated, ligated at 3' end with SR-adapter, reverse transcribed & PCR with NEBnext barcoded adapters
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
sequencing adapters from read1 were removed with CutAdapt (5'adapt: AGTCCGACGATC, 3'adapt:NNNNNAGATCGGAAGAG); UMI extracted with UMI-tools (pattern "NNNNN" located at 3'end)
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMultimapNmax=1, –outFilterScoreMinOverLread=0.9, –outFilterMatchNminOverLread=0.9)
mapped reads deduplicated with UMI-tools
read counts from Htseq, filtered for coding genes only
differential expression with DESeq2, translational efficiency with Riborex
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: tabular files of mapped read counts
Library strategy: RIBO-seq
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Nov 02, 2023 |
| 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 |
GPL23466 |
| Series (2) |
| GSE243206 |
Depletion of mRNA cap-binding protein eIF4E1 drives bradyzoite formation in Toxoplasma gondii [RIBO-seq] |
| GSE243207 |
Depletion of mRNA cap-binding protein eIF4E1 drives bradyzoite formation in Toxoplasma gondii |
|
| Relations |
| BioSample |
SAMN37395359 |
| SRA |
SRX21776554 |
