|
| Status |
Public on Apr 10, 2024 |
| Title |
eIF1-2-KO_tachyzoite_RIBOseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ME49deltaKu80deltaeIF1.2
|
| Organism |
Toxoplasma gondii |
| Characteristics |
cell line: ME49deltaKu80deltaeIF1.2
cell type: tachyzoites
treatment: DMEM pH7.4, 5%CO2
|
| Treatment protocol |
control is DMEM pH7.4, 10% FBS, 5% CO2; treatment is RPMI pH8.3, 3% FBS, amibent CO2
|
| Growth protocol |
4x10^7 parasites innoculated and grown in confluent human foreskin fibroblasts in DMEM-pH7.4+10%FBS (no antibiotic) for 2h prior to switching to fresh DMEM or to RPMI-pH8.3+3%FBS+ambient CO2 for 48h
|
| 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 collected by ultracentrifugation on a sucrose cushion. 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 eukaryotic Ribo-minus kit , 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)
in silico removal of reads mapping to toxoplasma rRNa & tRNA with bowtie2
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax 0.1, –outFilterScoreMinOverLread=0.9, –outFilterMatchNminOverLread=0.9)
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 |
Oct 19, 2023 |
| Last update date |
Apr 10, 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 |
GPL23466 |
| Series (1) |
| GSE245775 |
Translation initiation factor eIF1.2 orchestrates Toxoplasma gondii differentiation by regulating stage-specific gene expression |
|
| Relations |
| BioSample |
SAMN37883693 |
| SRA |
SRX22145097 |
