|
| Status |
Public on Apr 22, 2010 |
| Title |
3td-SMN vs 3WT |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA from td-SMN strain
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: td-SMN
|
| Growth protocol |
Both wild type and mutant strains were grown at 25°C in YES medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were purified with Tri-Reagent (Sigma) and treated with RQ1 RNAse-free DNAse.
|
| Label |
biotin
|
| Label protocol |
Labelling was done according to the Affymetrix tiling array manufacturer instructions starting from 10μg of total RNA
|
| |
|
| Channel 2 |
| Source name |
RNA from wild type strain
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: wild type
|
| Growth protocol |
Both wild type and mutant strains were grown at 25°C in YES medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were purified with Tri-Reagent (Sigma) and treated with RQ1 RNAse-free DNAse.
|
| Label |
biotin
|
| Label protocol |
Labelling was done according to the Affymetrix tiling array manufacturer instructions starting from 10μg of total RNA
|
| |
|
| |
| Hybridization protocol |
Approximately 6μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000 7G
|
| Description |
none
|
| Data processing |
Data were processed with the TAS software with the following settings: Scale to target intensity 100; Signal scale Log2; p-value scale -10Log10; Bandwidth 40; Two sided test type; PM/MM intensities.Data were analyzed by two sample comparison, normalized using quantile normalization plus scaling. Both control and treatment groups were normalized together.
|
| |
|
| Submission date |
Jul 08, 2009 |
| Last update date |
Apr 22, 2010 |
| Contact name |
johann Soret |
| E-mail(s) |
johann.soret@igmm.cnrs.fr
|
| Organization name |
CNRS
|
| Department |
Institut de Genetique Moleculaire
|
| Lab |
Assembly and traffic of ribonucleoproteins
|
| Street address |
1919, route de Mende
|
| City |
Montpellier |
| ZIP/Postal code |
34293 |
| Country |
France |
| |
|
| Platform ID |
GPL7715 |
| Series (1) |
| GSE17010 |
Differential pre-mRNA defects in fission yeast carrying a temperature degron allele of the SMN gene |
|
