|
| Status |
Public on Oct 22, 2009 |
| Title |
A. niger Xylose rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Aspergillus niger grown on xylose medium
|
| Organism |
Aspergillus niger |
| Characteristics |
Strain: A. niger BO 1. Medium: Minimal xylose-based medium. Growth conditions: Controlled fermenter kept at pH 4.5. Sampling time: mid-late exponential phase. Replicate no: 3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.
|
| Label |
Biotin
|
| Label protocol |
Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| |
|
| Hybridization protocol |
Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.
|
| Scan protocol |
Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.
|
| Description |
n/a
|
| Data processing |
Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).
|
| |
|
| Submission date |
Dec 08, 2008 |
| Last update date |
Oct 22, 2009 |
| Contact name |
wanwipa vongsangnak |
| E-mail(s) |
wanwipa@chalmers.se
|
| Phone |
+46 7723847
|
| Organization name |
Chalmers University of Technology
|
| Department |
Department of Chemical and Biological Engineering
|
| Lab |
Systems Biology
|
| Street address |
Kemivägen 10
|
| City |
Gothenburg |
| ZIP/Postal code |
SE-412 96 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5975 |
| Series (1) |
| GSE13868 |
Genome-wide analysis of maltose utilization and regulation in aspergilla |
|
