|
| Status |
Public on Jan 01, 2011 |
| Title |
RIL_WN60 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans Recombinant Inbred Lines
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
|
| Treatment protocol |
Four replicate dishes of synchronized eggs for each RIL were kept at 24 C until L3 was reached. The nematodes were then collected and frozen in liquid nitrogen.
|
| Growth protocol |
All RILs were reared on NGM agar plates seeded with the OP50 strain of E. coli as a food source. Stock cultures of OP50 were stored at -80 C, and the bacterial cultures were grown in autoclaved LB medium (10 g peptone, 10 g yeast extract, 5 g NaCl/l water) for 16 h at 37 C and shaken at 150 rpm. RIL populations were started with only nonmated hermaphrodites and screened regularly to remove any occurring males. Experiments were carried out with nematodes belonging to the L3 life stage. To determine the entry into this stage, the size of the gonads and vulva were monitored. Populations of each of the RILs were bleached (0.5 M NaOH, 1% hypochlorite) to collect synchronized eggs, which were then inoculated onto fresh dishes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The frozen nematode samples were ground and RNA was extracted using the Trizol method, and cleaned up with the RNeasy Micro kit (Qiagen, http://www1.qiagen.com/). RNA concentration and quality was measured with a NanoDrop spectrophotometer (http://www.nanodrop.com). Ds-cDNA synthesis with Affymetrix GeneChip WT double-stranded cDNA Synthesis Kit. To clean the cDNA we used the GeneChip Sample Cleanup Module from Affymetrix.
|
| Label |
biotin
|
| Label protocol |
For the fragmentation and labeling we used GeneChip WT double stranded DNA Terminal Labeling Kit.
|
| |
|
| Hybridization protocol |
DNase I-treated and control samples were hybridized to the Affymetrix GeneChip® C. elegans Tiling 1.0R Array, which contains ~3.2 million perfect match/mismatch probe pairs tiled through the Watson strand of the entire non-repetitive C. elegans genome. The probes are tiled at an average distance of 25 bp, as measured from the central position of adjacent 25-mer oligonucleotide probes.
|
| Scan protocol |
GeneChip® Scanner 3000 Quick Reference Card or user’s manual
|
| Description |
Gene expression data from worm belonging to the L3 life stage
|
| Data processing |
The data has been quantile normalized.
|
| |
|
| Submission date |
Apr 22, 2009 |
| Last update date |
Jan 01, 2011 |
| Contact name |
Yang Li |
| Organization name |
Groningen Bioinformatics Center
|
| Street address |
Kerklaan 30
|
| City |
Haren(GN) |
| ZIP/Postal code |
9751NN |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL5634 |
| Series (1) |
| GSE15778 |
Global genetic robustness of the alternative splicing machinery in C. elegans |
|
