|
| Status |
Public on Jan 31, 2011 |
| Title |
Aspergillus niger AreBKO, glucose, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
AreBKO-Glucose
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: ATCC 1015
genotype/variation: areB complete deletion mutant
tissue: Fungal biomass
|
| 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 niger strains were grown in 2.7 L batch cultivations with pH, agitation and temperature control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 1 g of fungal biomass was used for total RNA isolation using the Qiagen RNeasy Mini Kit according to the protocol for isolation of total RNA from plants and fungi.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA was prepared from approximately 1 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 GeneArray Scanner 3000 7G. Scanned probe array images (.DAT files) were converted into .CEL files using the Affymetrix GeneChip Operating Software.
|
| Description |
Gene expression data from A. niger areB complete deletion strain grown in batch cultivations
|
| Data processing |
Affymetrix CEL data files were preprocessed using the statistical language R version 2.9.2 and Bioconductor version 2.4. 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 |
Mar 23, 2010 |
| Last update date |
Jan 31, 2011 |
| 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) |
| GSE21015 |
Expression data from batch cultivations with the acidogenic Aspergillus niger wild type strain ATCC 1015 and the areB complete deletion strain constructed using ATCC 1015 as background strain with glucose or glycerol as carbon sources. |
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