|
| Status |
Public on Feb 27, 2009 |
| Title |
Anidulans_phk6msa_xylose_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Mycelium from the exponential phase of a batch cultivation on a xylose medium. Replicate 3.
|
| Organism |
Aspergillus nidulans |
| Characteristics |
Strain: A. nidulans with a phk K/O and inserted 6msa. Carbon Source: Xylose. Replicate: 3rd.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cultures were harvested at the late exponential phase at a biomass dry-weight concentration of 6-7 g/L. Mycelium was harvested by filtration through sterile Mira-Cloth (CalBioChem). The mycelium was quickly dried by squeezing, and subsequently frozen in liquid nitrogen. Samples were stored at -80 oC until they were used for RNA extraction. Total RNA was isolated using the Qiagen RNeasy Mini Kit, according to the protocol for isolation of total RNA from plant and fungi.
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard expression labeling according to the Affymetrix GeneChip Expression Analysis Technical Manual
|
| |
|
| Hybridization protocol |
Approximately 15 μg of fragmented cRNA was hybridized following the Affymetrix GeneChip Expression Analysis protocol.
|
| Scan protocol |
The array was scanned on an Agilent GeneArray Scanner 3000
|
| Description |
Part of a study of polyketide production in Aspergillus nidulans.
|
| Data processing |
The scanned probe array images (.DAT files) were converted into CEL data files using the GeneChip Operating Software from Affymetrix, and subsequently preprocessed using the statistical language and environment R (www.R-project.org) version 2.5. The probe intensities were normalised for background noise with the robust multiarray average (RMA) method using only perfect match (PM) probes. Normalisation was performed subsequently using the quantiles algorithm. Gene expression values were calculated from the PM probes with the medianpolish summary method.
|
| |
|
| Submission date |
Sep 19, 2008 |
| Last update date |
Feb 27, 2009 |
| 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 (1) |
| GSE12859 |
Studies on the production of fungal polyketides in Aspergillus nidulans using systems biology tools |
|
