|
| Status |
Public on Jun 18, 2012 |
| Title |
wt_total RNA_3 |
| Sample type |
RNA |
| |
|
| Source name |
wt_total RNA
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
genotype/variation: wild type
developmental stage: young adult
tissue: whole worm lysate
|
| Treatment protocol |
Worm lysates were prepared in extraction buffer and subjected to sucrose density gradient ultracentrifugation; the gradients were fractionated into 12 samples
|
| Growth protocol |
Worms were grown until the young adult stage, washed in cold M9, and washed and frozen in washing buffer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from total and polysomal sucrose fractions was extracted using Trizol
|
| 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 |
Oct 19, 2011 |
| Last update date |
Jun 18, 2012 |
| Contact name |
Dimos Gaidatzis |
| E-mail(s) |
[email protected]
|
| Organization name |
Friedrich Miescher Institute
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL5634 |
| Series (2) |
| GSE33083 |
Polysome profiling of wild-type and gld-1 mutant animals |
| GSE33084 |
GLD-1 mRNA regulation |
|
