|
| Status |
Public on Feb 10, 2008 |
| Title |
Aniger_Xylose_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
A. niger mycelium grown on a 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 |
-
|
| Data processing |
Affymetrix CEL-data files were preprocessed using the statistical language and environment R, 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 quantiles algorithm (Bolstad, 2003). 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 |
Oct 09, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Mikael R Andersen |
| E-mail(s) |
mr@bio.dtu.dk
|
| Organization name |
Technical University of Denmark
|
| Department |
BioCentrum-DTU
|
| Lab |
Center for Microbial Biotechnology
|
| Street address |
Søltofts plads, bygn 223
|
| City |
Kgs. Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL5975 |
| Series (2) |
| GSE9276 |
A tri-species Aspergillus array (niger arrays) |
| GSE9298 |
A tri-species Aspergillus array |
|
