|
| Status |
Public on Jan 31, 2011 |
| Title |
Aspergillus niger ATCC 1015, glycerol, biological rep1c |
| Sample type |
RNA |
| |
|
| Source name |
Fungal biomass, ATCC 1015, glycerol
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: ATCC 1015 wild type
carbon source: glycerol
|
| 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 ug of total RNA according to the protocol described in the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).
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| |
|
| Hybridization protocol |
Approximately 15 ug 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 ATCC 1015 strain grown in batch cultivations.
This sample was included in the CreA deletion mutant dataset.
|
| 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 across subsets of samples (12 samples for each comparison), i.e., each gene deletion strain grown in triplicate on glucose or glycerol carbon sources was compared to the wild type strain ATCC 1015 grown in triplicate on the same carbon sources. The same six ATCC 1015 CEL files were used for each normalization. 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.
The Sample data tables include the gene expression indexes calculated for the datasets used for each ANOVA comparison.
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| |
|
| Submission date |
Jan 19, 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) |
| GSE19952 |
Expression data from batch cultivations of Aspergillus niger wild type and adrA, facB and creA deletion mutants |
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