|
| Status |
Public on Apr 14, 2024 |
| Title |
Ribo-seq in exponential growing cells replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Trypanosoma cruzi |
| Characteristics |
strain: Dm28c
cell type: whole organism
genotype: WT
treatment: cells (epimastigote stage) in exponential growth conditions
|
| 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 |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Ribo-seq in exponential growing cells replicate 2
Sample 58
|
| 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)
Library strategy: Ribo-seq
|
| |
|
| 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 |
SAMN40932331 |
| SRA |
SRX24226180 |
