|
| Status |
Public on Mar 19, 2014 |
| Title |
N2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
day 0 adult without bearing eggs
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotype: N2
|
| Treatment protocol |
Worms were synchronized by two rounds of bleaching.
|
| Growth protocol |
Worms were grown at 20C on OP50 plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed as described in Heestand et al. 2013
Described in Heestand et al. 2013
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample A
|
| Data processing |
Sequencing reads were trimmed to remove adapter sequence using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/)
The trimmed reads were aligned to the C. elegans reference genome (WBcel215.67) using tophat version 1.3 (Trapnell, Pachter & Salzberg 2009) with option −g1 to ensure unique mapping
The number of reads mapping to each Ensemble gene was counted with htseq-count (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html#count).
Statistical analysis was performed with the bioconductor package Deseq (Anders, Huber 2010).
Significant differentially expressed genes were compiled from the Deseq-result as follows: FDR<0.05, mean normalized count >10 and absolute Foldchange (FC) >1.5.
Genome_build: WBcel215.67
Supplementary_files_format_and_content: htseq-count-table.txt contains non-normalized read counts assigned to genes.
|
| |
|
| Submission date |
Mar 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Corinna Klein |
| E-mail(s) |
cklein@age.mpg.de
|
| Organization name |
Max Planck Institute for Biology of Ageing
|
| Street address |
Joseph-Stelzmann-Straße 9b
|
| City |
Köln |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE55988 |
mRNA profile in DR-related mutants |
|
| Relations |
| BioSample |
SAMN02690810 |
| SRA |
SRX494547 |
