|
| Status |
Public on Mar 29, 2012 |
| Title |
Aniger_Xylan_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
A. niger mycelium grown on a xylan medium
|
| Organism |
Aspergillus niger |
| Characteristics |
Strain: BO-1
Carbon source: Xylan
Sample time: Mid-exponential phase
Cultivation: Shake-flask
Replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
As described in Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92.
PMID: 18332432
|
| Label |
Affymetrix standard
|
| Label protocol |
Affymetrix standard
|
| |
|
| Hybridization protocol |
Affymetrix standard
|
| Scan protocol |
As described in Andersen MR, Vongsangnak W, Panagiotou G, Salazar MP, Lehmann L, Nielsen J. A trispecies Aspergillus microarray: comparative transcriptomics of three Aspergillus species. Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92.
PMID: 18332432
|
| Description |
Part of a study of transcriptional profiling across six carbon-sources.
|
| Data processing |
Affymetrix CEL-data files were preprocessed by using the statistical language and environment R (R Development Core Team, 2007) version 2.6.1. The probe intensities were normalized for background by using the robust multiarray average method (Irizarry, 2003) by using only perfect match (PM) probes. Normalization was performed subsequently by 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 |
Jun 29, 2008 |
| Last update date |
Mar 29, 2012 |
| 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) |
| GSE11930 |
Network-based analysis of carbohydrate-active gene transcription in Aspergillus niger |
|
