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Sample GSM8198386 Query DataSets for GSM8198386
Status Public on Apr 14, 2024
Title eIF4E4 immunoprecipitation in nutritional stress replicate 1
Sample type SRA
 
Source name whole organism
Organism Trypanosoma cruzi
Characteristics strain: Dm28c
cell type: whole organism
genotype: WT
treatment: cells (epimastigote stage) in nutritional stress for two hours
Treatment protocol Nutritional stress was induced by incubation in TAU media for 2 hours
Metacyclic trypomastigotes were differentiated by incubation in TAU for 2 hours, in TAU3AAG for 4 days and subsequently purified by anion exchange chromatography
Growth protocol Trypanosoma cruzi Dm28c cells were mantained in LIT supplemented in 10% FCS and antibiotics at 28C 5% CO2
Extracted molecule other
Extraction protocol RNA was extracted from the beads (RIP-seq), directly from the cells (RNA-seq) or from the polysomal fraction (Ribo-seq)
RNA libraries were prepared with TruSeq Stranded mRNA kit following manunfacter's protocols
 
Library strategy RIP-Seq
Library source other
Library selection other
Instrument model Illumina HiSeq 2500
 
Description eIF4E4 immunoprecipitation (endogenous using specific antibodies) in nutritional stress replicate 1
Sample 16
Data processing Sequencing reads were mapped against the T. cruzi Dm28c genome with STAR v2.7.10a with default parameters
Gene counts were obtained for uniquely mapped reads with featureCounts v2.0.1 from the Subread package
To identify mRNAs enriched in the immunoprecipitation eluate relative to the control, the differential expression analysis DESeq2 v1.34.0was used
Assembly: Ensembl Assembly ASM317710v1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (numbered from 1 to 66 according to library names)
 
Submission date Apr 11, 2024
Last update date Apr 14, 2024
Contact name Bernardo Papini Gabiatti
E-mail(s) bgabiatti@gmail.com
Organization name University of Würzburg
Street address Sanderring 2
City Würzburg
ZIP/Postal code 97070
Country Germany
 
Platform ID GPL34379
Series (1)
GSE263777 Two distinct Trypanosoma eIF4F complexes co-exist, bind different mRNAs and are regulated during nutritional stress
Relations
BioSample SAMN40932373
SRA SRX24226151

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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