|
| Status |
Public on Apr 23, 2013 |
| Title |
Nr35 48h H20 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
total RNA from whole animals
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
developmental stage: Adult (48 hours after L4)
treatment: control plate
tissue: whole organism
|
| Treatment protocol |
Treatment of C. elegans was carried out on NGM agar plates containing 100nM arsenite or the respective solvent control (H2O) and spotted with heat-inactivated OP50 E. coli. Thereby, agar plates were prepared from the same batch of NGM Agar, whereas treatment plates were supplemented with the arsenite and control plates with the corresponding solvent as described (Schmeisser et al. 2011).
|
| 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 |
RNA isolation was performed using a commercially available kit (Qiagen, Hilden, Germany, Rneasy Mini Kit) based on the phenol-chloroform extraction method according to the manufacturer’s instructions. 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 5 μg of total RNA per sample was processed using Illumina’s mRNA-Seq 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 Genome Analyzer IIx |
| |
|
| Description |
Nr35
|
| Data processing |
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Bowtie vs. the C.elegans genome and a splice site data set created using UCSC's RefSeq annotation
Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor
Calculation of RPKM values for each transcript and gene from RefSeq annotation (see ce_Nr35-38_counts_rpkm.xls)
Genome_build: ce6\WBcel235
Supplementary_files_format_and_content: RPKM
|
| |
|
| Submission date |
Apr 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
JenAge Project |
| E-mail(s) |
[email protected]
|
| Organization name |
Leibniz Institute for Age Research - Fritz Lipmann Institute
|
| Street address |
Beutenbergstr. 11
|
| City |
Jena |
| ZIP/Postal code |
D-07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13776 |
| Series (1) |
| GSE46257 |
Deep sequencing of endogenous mRNA from Caenorhabditis elegans in the presence and absence of arsenite |
|
| Relations |
| BioSample |
SAMN02054426 |
| SRA |
SRX270953 |
