|
| Status |
Public on Oct 03, 2014 |
| Title |
Manganese depleted, biological replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Biomass from pseudo steady state
|
| Organism |
Aspergillus niger |
| Characteristics |
experimental condition: Manganese depleted
|
| Treatment protocol |
The growth of fungal cultures was rapidly terminated by cooling in an ice-water bath. The biomass was immediately separated from the culture supernatant by centrifugation in 500 ml centrifuge bottles for 10 minutes at 4oC and 10,000 g. The biomass was ransferred from the centrifugation bottles to Corning 50 ml polypropylene centrifugation tubes, washed with 50 ml ice-cold 50mM phosphate buffer once, and centrifuged again at 9,000 g and 4oC for 5 min. The biomass was immediately frozen in liquid N2 and then stored at -80oC until use.
|
| Growth protocol |
Nine one-liter baffled-flasks containing 250 ml of citric acid production media with 10 ppb Mn2+ were used. Each flask was inoculated with 1 × 10^6 spores/ml and incubated for thirty hours at 30C and 220 rpm to obtain large-amount biomass in pelleted morphology, then 1000 ppb Mn2+ was added to three of the flasks to induce filamentous growth and the same amount of H2O was added into another three flasks for control.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the above A. niger biomasses according to the modified acid-guanidinium isothiocyanate phenol-chloroform extraction method previously described (Chomczynski and Sacchi 1987, Dai et al 2000), and the total RNA concentration was quantified spectrophotometrically. Polyadenylated RNA was isolated from the total RNA with the Oligotex kit (QIAGEN, Valencia, CA, USA).
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled cRNA was prepared from total RNA according to the Affymetrix GeneChip Expression Analysis Technical Manual
|
| |
|
| Hybridization protocol |
hybridized to the 3AspergDTU GeneChip (PMID: 18332432 )
|
| Scan protocol |
A GeneChip Fluidics Station FS-400 was applied for hybridization followed by scanning using a GeneChip Scanner 3000. The scanned probe array images (.DAT files) were converted into .CEL files using the GeneChip Operating Software
|
| Description |
SAMPLE 5
|
| Data processing |
The analysis of the affymetrix CEL-data files was carried out accordingly to the protocol described in PMID: 19409083
probe group file: 3AspergDTU GeneChip (PMID: 18332432 )
|
| |
|
| Submission date |
Oct 02, 2014 |
| Last update date |
Oct 03, 2014 |
| Contact name |
Lars Poulsen |
| E-mail(s) |
lpoulsen.dk@gmail.com
|
| Organization name |
Technical University of Denmark
|
| Department |
Department of Systems Biology
|
| Street address |
Soltofts Plads 1
|
| City |
Kgs. Lyngby |
| ZIP/Postal code |
2800 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL5975 |
| Series (1) |
| GSE61985 |
Correlating citric acid formation and manganese limitation in Aspergillus niger using transcriptome and proteome analysis |
|
