|
| Status |
Public on Feb 12, 2019 |
| Title |
age-1(hx546); gas-1(fc21) 5 |
| Sample type |
SRA |
| |
|
| Source name |
whole body
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
Stage: L4
|
| Growth protocol |
Nematodes were synchronized via hypochlorite solution treatment and grown at 20°C on standard NGM plates and fed with OP50 E. coli bacteria
|
| Extracted molecule |
total RNA |
| Extraction protocol |
L4 stage nematodes were collected in M9 buffer, washed 3x and stored at -80°C until needed. RNA was extracted with an RNeasy kit (QIAGEN) as per the manufacturer's instructions
approximately 100 ng of total RNA was used for library construction (TruSeq Stranded mRNA library Prep Kit, Illumina). Sequencing was performed with a HiSeq4000 HighOutput Mode Illumina platform (1x50 bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Demultiplexing of the sequencing reads was performed with Illumina CASAVA (1.8.2). Adapters were trimmed with Skewer (version 0.1.116) (Jiang et al. 2014).
Trimmed raw reads were aligned to the C. elegans reference genome (PRJNA13758) using STAR (version 2.4.0h) (Dobin et al. 2013).
Further analyses were performed with the Cufflinks Tool Suite (Version 2.1.1) (Roberts et al. 2011; Trapnell et al. 2010): Cufflinks was used to count mapped reads.
FPKM values were computed with Cuffdiff (Trapnell et al. 2013) using the “pooled-variance“ model, “geometric“ normalization and “multi-read-correct“ option.
The quality of fastQ files was analyzed with FASTQC (Version 0.10.1) (Andrews 2010).
Genome_build: PRJNA13758
Supplementary_files_format_and_content: excel files including FPKM values for each sample
|
| |
|
| Submission date |
Nov 25, 2018 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Daniele Bano |
| Organization name |
DZNE
|
| Street address |
Sigmund-Freud-Strasse 27
|
| City |
Bonn |
| ZIP/Postal code |
53127 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22765 |
| Series (1) |
| GSE122902 |
Transcriptome of a long-lived mutant nematode with severe mitochondrial deficiency |
|
| Relations |
| BioSample |
SAMN10474906 |
| SRA |
SRX5059396 |
