|
| Status |
Public on Jan 31, 2018 |
| Title |
cde-1 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: cde-1
agent: Orsay virus
|
| Treatment protocol |
Orsay virus infection as described above.
|
| Growth protocol |
Approximately 200 cde-1 (tm1021) mutants or N2 animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological triplicates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines.
mRNA libraries were prepared using the NEBNext Ultra directional RNA library kit (NEB) with poly(A) selection and deep sequencing was produced with an Illumina HiSeq machine (single read 50).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
For differential expression analysis, genes were only included in the analysis if they had at least 1 count per million in all of the control samples or all of the experiment samples.
After applying this filter, differentially expressed genes were then called using EdgeR (Robinson, et al. 2010).
For the correlation matrix, Pairwise Pearson correlation values were calculated between all samples.
genome build: C.elegans WS220 / Ce10.
Supplementary_files_format_and_content: Raw Counts
|
| |
|
| Submission date |
Jan 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Charles Bradshaw |
| Organization name |
University of Cambridge
|
| Department |
Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL18730 |
| Series (1) |
| GSE76901 |
mRNA sequencing in cde-1 mutants versus WT C. elegans infected by the Orsay virus |
|
| Relations |
| BioSample |
SAMN04417256 |
| SRA |
SRX1531893 |
