|
| Status |
Public on Nov 05, 2012 |
| Title |
WT |
| Sample type |
SRA |
| |
|
| Source name |
worm total lysates
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2 Bristol; wildtype
genotype: wild type
age: young adult
|
| Treatment protocol |
Worms were incubated on NGM plates in sealed plastic bags for 5 hours at 35°C in a thermostate controlled waterbath
|
| Growth protocol |
Worms were grown on NGM at 20°C with E. coli OP50 as food source
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA-isolation was carried out with RNAiso-G, a modified Guanidin-isothiocyanate/phenol RNA-extraction method, and a subsequent cleanup with RNeasy® mini kit and on-column DNAseI treatment
mRNA was purified using oligo-(dT)-magnetic beads, and first and second strand cDNA-synthesis was carried out using random hexamer primers. Samples were ligated with sequencing adaptors and sequenced with Illumina HiSeq2000 with a minimum 10 Megareads per sample and a sequencing quality of more than 98% clean reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequencing quality determination with Illumina GA Pipeline
Filtering: Remove reads with adaptors, remove reads in which unknown bases are more than 10%, remove low quality reads
Alignment to reference sequence using soap2, no more than 2 mismatches are allowed in the alignment
Calculation of gene expression levels by using the RPKM (Reads Per kb per Million reads) method
Genome_build: Wormbase release WS223
Supplementary_files_format_and_content: tab-delimited .txt with unique reads number, gene lenth, gene coverage and RPKM-values for annotated genes in KU25 and N2
|
| |
|
| Submission date |
Sep 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Rüdiger J Paul |
| E-mail(s) |
paulr@uni-muenster.de
|
| Organization name |
Westfälische Wilhelms-Universität Münster
|
| Department |
Institut für Zoophysiologie
|
| Lab |
Paul
|
| Street address |
Schlossplatz 8
|
| City |
Münster |
| ZIP/Postal code |
48143 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE41205 |
Influence of p38 MAPK (PMK-1) on the heat stress response of C. elegans |
|
| Relations |
| SRA |
SRX189885 |
| BioSample |
SAMN01731140 |
