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| Status |
Public on Oct 06, 2021 |
| Title |
RNA sequencing of wild type C.elegans exposed to Haptoglossa zoospora for 6 or 12 hours |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We aimed to investigate the C. elegans response to Haptoglossa zoospora infection. To this end we performed RNA sequencing using the illumina Hiseq 2500 platform on infected animals at the L4 stage of development after 6hours and 12 hours of pathogen exposure and uninfected animals at the same time points . The sequence reads, generated by Imperial College London sequencing facility (Hammersmith campus) that passed quality controls were aligned to the most recent C. elegans (WBcel235) transcriptome using the pseudoalignment tool Kallisto. The generated abundance files were analysed using an R pipeline for Sleuth. Differentially expressed genes with a p value <0.01 and FDR value <0.1 were isolated from the dataset and compared to genes induced in infections by other C. elegans pathogens including the oomycete Myzocytiopsis humicola. The result of this comparison revealed conserved features underlying oomycete detection by C. elegans.
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| Overall design |
RNA sequencing profiles of L4 control or Haptoglossa exposed C. elegans
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| Contributor(s) |
Fasseas MK, Grover M, Barkoulas M |
| Citation(s) |
34722333 |
| |
| Submission date |
Jun 01, 2021 |
| Last update date |
Nov 04, 2021 |
| Contact name |
Michalis Barkoulas |
| Organization name |
Imperial College London
|
| Department |
Faculty of Natural Sciences
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| Lab |
Barkoulas
|
| Street address |
Sir Alexander Fleming Building, Imperial College RD
|
| City |
London |
| ZIP/Postal code |
Sw7 2Az |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL18245 |
Illumina HiSeq 2500 (Caenorhabditis elegans) |
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| Samples (11)
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| Relations |
| BioProject |
PRJNA734346 |
| SRA |
SRP322193 |
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