|
| Status |
Public on Jan 01, 2019 |
| Title |
Flu4 |
| Sample type |
SRA |
| |
|
| Source name |
whole organism
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: wildtype (N2)
treatment: fluphenazine
tissue: whole organism
|
| Treatment protocol |
Synchronized L4 worms were placed on stress plates (200uM fluphenazine, 200uM cantharidin, 10uM bortezomib or 25uM bortezomib) and collected the next day. For rpn-6 RNAi treatment, synchronized L3 worms were placed on RNAi plates and collected at day 1. For starvation, synchronized worms were placed on empty plates 15h prior collection. Control worms were not treated.
|
| Growth protocol |
Synchronized worms were grown on 20°C until day 1 of adulthood. Food source: E. coli OP50
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA isolation followed the standard procedures using Trizol reagent (Invitrogen). RNA was subsequently purified using the RNeasy kit (Qiagen).
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline
Sequenced reads mapped to C elegans
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: caenorhabditis_elegans
Supplementary_files_format_and_content: tab-delimited file include FPKM values for each Sample
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Thorsten Hoppe |
| E-mail(s) |
[email protected]
|
| Organization name |
CECAD Cologne and Institute for Genetics
|
| Department |
Institut für Genetik
|
| Lab |
Hoppe Lab
|
| Street address |
Joseph-Stelzmann-Str. 26
|
| City |
Cologne |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13776 |
| Series (1) |
| GSE124178 |
RNA-seq: WT under proteotoxic stress conditions |
|
| Relations |
| BioSample |
SAMN10620073 |
| SRA |
SRX5169891 |
