|
| Status |
Public on Jul 04, 2016 |
| Title |
wt.cm_2 |
| Sample type |
RNA |
| |
|
| Source name |
F. fujikuroi wildtype,CM
|
| Organism |
Fusarium fujikuroi |
| Characteristics |
genotype: wildtype
tissue: mycelia
media: complete media
|
| Treatment protocol |
Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction
|
| Growth protocol |
Strains were grown for three days on solid complete medium (CM) or solid synthetic ICI medium with 6 mM ammonium nitrate at 28 °C in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (InvitrogenTM) according to manufacturer´s instructions. Final clean-up was carried out with the NucleoSpin® RNA Clean-up Kit (Macherey Nagel, Düren, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).
|
| Label |
Cy3
|
| Label protocol |
Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.
|
| Data processing |
Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)
|
| |
|
| Submission date |
Apr 20, 2016 |
| Last update date |
Jul 04, 2016 |
| Contact name |
Ulrich Guldener |
| E-mail(s) |
u.gueldener@tum.de
|
| Organization name |
Technische Universität München
|
| Department |
Chair of genome-oriented bioinformatics
|
| Street address |
Maximus-von-Imhof-Forum 3
|
| City |
Freising |
| State/province |
Bavaria |
| ZIP/Postal code |
D-85354 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21751 |
| Series (2) |
| GSE80477 |
Knock-down of the methyltransferase Kmt6 reliefs H3K27me3 and induces expression of cryptic otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi [gene expression] |
| GSE80479 |
Knock-down of the methyltransferase Kmt6 reliefs H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi |
|
