|
| Status |
Public on Nov 30, 2011 |
| Title |
Mixed-stage embryos from hpl-2(tm1489) strain, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans embryos, mixed stage, hpl-2(tm1489) strain
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain/genotyp: hpl-2(tm1489)
Stage: Embryos
|
| Treatment protocol |
All strains were grown at 20 degrees. Embryos were recovered by bleaching of gravid adults. Synchronized cultures of L3 stage worms were obtained by bleaching and L1 starving. Staging was carried out according to vulval and somatic gonad development (28 to 29 hours).
|
| Growth protocol |
Wild-type and mutant strains were grown on NG Agar plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Following trizol extraction, RNA was further purified using RNAEasy column (Qiagen) according to manufacturer's protocol
|
| Label |
Biotin
|
| Label protocol |
300ng total RNA were amplified with the GeneChip Whole Transcript Amplified Double-Stranded Target Assay (Affymetrix) according to the manufacturer's instructions; 7ug of sense cDNA fragmented and labeled with the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
7ug fragmented and labeled cDNA were hybridized to GeneChip C. elegans Tiling 1.0R Arrays for 16h followed by washing with the fluidics protocol FS450_0001 on a Affymetrix washing station.
|
| Scan protocol |
Scanning was performed with Affymetix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader.
|
| Description |
Gene expression data from hpl-2(tm1489) mixed-stage embryos
|
| Data processing |
Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probesets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. The R code is available upon request. The CDF package is available as a Series Supplementary file [Ce25b_MR_v02.CDF]. RMA normalized expression values created with R/Bioconductor package affy using the attached CDF file [RMA_normalized_data.txt available as a Series Supplementary file]
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| |
|
| Submission date |
Nov 15, 2011 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Peter Meister |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Bern
|
| Department |
Institute of Cell Biology
|
| Street address |
Baltzerstrasse 4
|
| City |
Bern |
| ZIP/Postal code |
3012 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL5634 |
| Series (1) |
| GSE33700 |
Transcriptome analysis of hpl-2(tm1489) vs wild-type worms at mixed embryonic and third larval stages |
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