|
| Status |
Public on Oct 07, 2014 |
| Title |
Expression profile by RNA-seq of wild type or Caenorhabditis elegans mutant for the Werner syndrome gene ortholog treated with or without vitamin C |
| Organism |
Caenorhabditis elegans |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
In this study, we analyzed the impact of a mutation in the wrn-1 gene compared to wild type worms and the dietary supplementation of vitamin C on the global mRNA expression of the whole C. elegans by the RNA-seq technology.
|
| |
|
| Overall design |
Whole C. elegans mRNA profiles at the L4 stage of wild type and wrn-1(gk99) mutant animals treated with or without 10 mM ascorbate were generated by deep sequencing, in triplicate, using the HiSeq 2000 machine form Illumina. Detailed statistics on the quality of the reads were calculated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The 50 base pairs raw sequences were aligned on the C. elegans ce10/W220 genome with TopHat using the Ensembl annotations provided with the Illumina iGenomes. The htseq-count software (http://www-huber.embl.de/users/anders/HTSeq) was used to count the number of reads aligned to each gene. These counts were then normalized relative to the sequencing depth with DESeq.
|
| |
|
| Contributor(s) |
Lebel M |
| Citation(s) |
25346348 |
| Submission date |
Jan 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Michel Lebel |
| E-mail(s) |
michel.lebel@crchudequebec.ulaval.ca
|
| Phone |
(418) 525-4444
|
| Organization name |
Centre de Recherche du CHU de Québec
|
| Department |
Centre Hospitalier de l’Université Laval (CHUL)
|
| Lab |
Michel Lebel
|
| Street address |
2705 Laurier Blvd, Local T-2-04
|
| City |
Quebec |
| State/province |
Qc |
| ZIP/Postal code |
G1V 4G2 |
| Country |
Canada |
| |
|
| Platforms (1) |
| GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
|
| Samples (12)
|
|
| Relations |
| BioProject |
PRJNA235332 |
| SRA |
SRP035479 |
Less...
More...