|
| Status |
Public on Oct 21, 2009 |
| Title |
Aspergillus niger, glycerol, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Fungal biomass
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: BO1
|
| Treatment protocol |
Fungal biomass from each of the Aspergillus fermentation replicates was harvested in the mid exponential phase of growth, filtered, washed, dryed by squeezing, frozen in liquid nitrogen and stored at -80 °C until further processing.
|
| Growth protocol |
Aspergillus nidulans, Aspergillus oryzae and Aspergillus niger were grown in batch cultivations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A. niger and A. nidulans total RNA was isolated using the Qiagen RNeasy Mini Kit according to the protocol for isolation of total RNA from plant and fungi. A. oryzae total RNA was purified by using the Promega RNAgents Total RNA Isolation system following manufacturer’s recommendations.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA was prepared from approximately 5 mg of total RNA according to the protocol described in the Affymetrix GeneChipÒ Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).
|
| |
|
| Hybridization protocol |
Approximately 15 mg of fragmented cRNA was hybridized for 16 hr at 45 °C on the 3AspergDTU Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using an Agilent GeneArrayÒ Scanner 3000. Scanned probe array images (.DAT files) were converted into .CEL files using the Affymetrix GeneChip Operating Software.
|
| Description |
Gene expression data from A. niger grown in batch cultivations
|
| Data processing |
Affymetrix CEL data files were preprocessed using the statistical language R version 2.7.1 and Bioconductor version 2.2. Normalization was performed using the qspline algorithm and gene expression indexes were calculated from the PM probes with the median polish summary method. All statistical preprocessing methods were implemented in affy package using R scripts and limma package.
|
| |
|
| Submission date |
Apr 16, 2009 |
| Last update date |
Oct 21, 2009 |
| Contact name |
Margarita Salazar Peña |
| E-mail(s) |
margarita.salazar@chalmers.se
|
| Phone |
+46 (031) 7723876
|
| Fax |
+46 (031) 7723801
|
| Organization name |
Chalmers University of Technology
|
| Department |
Chemical and Biological Engineering
|
| Lab |
Systems Biology
|
| Street address |
Kemigården 4
|
| City |
Göteborg |
| ZIP/Postal code |
SE-412 96 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5975 |
| Series (1) |
| GSE15702 |
Expression data from batch cultivations with A. niger, A. oryzae and A. nidulans grown on glucose and glycerol |
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