|
| Status |
Public on Sep 13, 2013 |
| Title |
wt-jb015-k2-b vs. ref1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wt
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
genotype/variation: wt
|
| Growth protocol |
S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2% D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
yeast HTP RNA isolation for robot v2.0
|
| Label |
Cy5
|
| Label protocol |
All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).
|
| |
|
| Channel 2 |
| Source name |
refpool
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
genotype/variation: refpool
|
| Growth protocol |
S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2% D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
yeast RNA isolation for robotic amplification v1.0
|
| Label |
Cy3
|
| Label protocol |
All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).
|
| |
|
| |
| Hybridization protocol |
Tecan HS4800 hybridization
|
| Scan protocol |
Scanning of slides using Agilent G2565BA scanner.
|
| Data processing |
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.
A software package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. Author(s): Gordon Smyth. The limma R package version 2.12.0 is used. P-values are Benjamini-Hochberg FDR corrected.
|
| |
|
| Submission date |
Dec 21, 2012 |
| Last update date |
Sep 14, 2013 |
| Contact name |
Marian Groot Koerkamp |
| Organization name |
Princess Maxima Center for Pediatric Oncology
|
| Department |
Research
|
| Lab |
Drostlab
|
| Street address |
Heidelberglaan 25
|
| City |
Utrecht |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL11232 |
| Series (1) |
|
