|
| Status |
Public on Jun 18, 2012 |
| Title |
Mock RNAi 3 |
| Sample type |
RNA |
| |
|
| Source name |
young adult cytoplasmic extracts
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: wild type
developmental stage: young adult
RNAi construct: Mock RNAi
tissue: whole worm lysate
|
| Treatment protocol |
Cytoplasmic extracts were prepared as described in Wright et al, 2010
|
| Growth protocol |
Worms were grown until the young adult stage.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was Trizol extracted
|
| Label |
biotin
|
| Label protocol |
RNA was processed according to the GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual from Affymetrix, fragmented and Biotin labeled using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
hybridization was performed overnight for 16 h in a GeneChip hybridization oven (Affymetrix)
|
| Scan protocol |
Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader
|
| Description |
SAMPLE 3
|
| Data processing |
All tiling arrays were processed in R using bioconductor and the packages tilingArray and preprocessCore. The arrays were RMA background corrected and log2 transformed on the oligo level using the following command: expr <- log2(rma.background.correct(exprs(readCel2eSet(filenames,rotated=TRUE)))). We mapped the oligos from the tiling array (bpmap file from www.affymetrix.com) to the c.elegans genome assembly ce6 (www.genome.ucsc.edu) using bowtie allowing no error and unique mappig position. Expressions for individual transcripts were calculated by intersecting the genomic positions of the oligos with transcript annotation (WormBase WS190) and averaging the intensity of the respective oligos.
probe group file: probeId_to_tr_min10probes.tab
|
| |
|
| Submission date |
Mar 22, 2012 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
d.gaidatzis@fmi.ch
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL5634 |
| Series (2) |
| GSE33084 |
GLD-1 mRNA regulation |
| GSE36713 |
mRNA expression analysis in mock and cgh-1(RNAi) animals |
|
