|
| Status |
Public on Aug 09, 2013 |
| Title |
Nr102 H20 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA from whole animals, control plate
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole animal
developmental stage: Adult (48 hours after L4)
agent: control plate
|
| Treatment protocol |
Treatment of C. elegans was carried out on NGM agar plates containing 1nM nicotinic acid, 1 µM 1-MNA or the respective solvent control (H2O). All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound and control plates with water.
|
| Growth protocol |
Nematodes were grown and maintained on NGM agar plates according to standard protocol as described (Brenner et al. 1974)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Nr102
|
| Data processing |
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v1.4.1) vs. the C. elegans genome (WS220)
For counting the reads per gene (raw counts) the Python package HTSeq was used in mode ‘union’ together with the Ensembl gene annotation. Only uniquely mapable reads were regarded.
Raw counts were analyzed using the R Statistical Computing Environment. RPKM values were calculated for each gene from the annotation (see ce_Nr101-109_counts_rpkm.xls)
Genome_build: WS220
|
| |
|
| Submission date |
Aug 08, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marco Groth |
| E-mail(s) |
dnaseq@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE49662 |
Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of 1-methylnicotinamide (MNA) and nicotinic acid (NA) |
|
| Relations |
| BioSample |
SAMN02313974 |
| SRA |
SRX332741 |
