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Status |
Public on Apr 14, 2024 |
Title |
eIF4E4 immunoprecipitation in nutritional stress replicate 1 |
Sample type |
SRA |
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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
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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
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Library strategy |
RIP-Seq |
Library source |
other |
Library selection |
other |
Instrument model |
Illumina HiSeq 2500 |
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|
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)
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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 |