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| Status |
Public on Oct 07, 2014 |
| Title |
A.niger grown without B.subtilis rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
A.niger grown without B.subtilis at 4 hours
|
| Organism |
Aspergillus niger |
| Characteristics |
strain: CB 119.1
|
| Treatment protocol |
Mycelium from three A. niger cultures in absence and in presence of B. subtilis was pooled on Miracloth and immediately frozen in liquid nitrogen.
|
| Growth protocol |
Aspergillus niger CB 119.1 was inoculated at 104 spores/ml and cultivated in TY medium (1% Bacto tryptone, 0.5% Bacto yeast, 0.5% NaCl, and 0.1 mM MnCl2) at 30 ºC, 250 rpm for 15 hours. For co-cultivation, B. subtilis was subsequently added the pre-cultures at a final concentration of 5•106 cfu/mL. The shaken co-cultivations were incubated at 30 ºC, 150 rpm for 2-40 hours before samples were taken at 4h for Microarray.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using TRIzol® Plus RNA Purification Kit (Sigma-Aldrich) according to the instructions of the manufacturer. RNA quantity and quality were determined on a Nanodrop spectrophotometer, and integrity was tested on an Agilent 2100 Bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled antisense cRNA was produced from 2 μg of total RNA with the Eukaryotic One-Cycle Target Labeling kit (Affymetrix; www.affymetrix.com).
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| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA was hybridized to Affymetrix A. niger Genome Gene chips (GPL6758). GeneChips were washed and stained in an automated process.
|
| Scan protocol |
GeneChips were scanned according to Affymetrix protocol.
|
| Description |
Gene expression data from A.niger grow without B.subtilis 4h
|
| 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).
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| |
|
| Submission date |
Apr 18, 2013 |
| Last update date |
Oct 08, 2014 |
| Contact name |
miaomiao Zhou |
| E-mail(s) |
miaomiaozhou88@hotmail.com
|
| Phone |
+ 31 (0)30 2122600
|
| Organization name |
centre of fungal biodiversity, Utrecht, KNAW
|
| Department |
fungal physiology
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584 CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6758 |
| Series (1) |
| GSE46187 |
Attachment of Bacillus subtilis to the hyphae of Aspergillus niger results in altered metabolism and defense mechanisms in both partner |
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