|
| Status |
Public on Jul 23, 2014 |
| Title |
AM1 Parafilm 12h, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
U. maydis AM1 culture sprayed on parafilm surface
|
| Organism |
Ustilago maydis |
| Characteristics |
cellular differentiation: filamentous cells
genotype: AM1
time: 12 h
treatment: incubated for 12h on hydrophobic surface
|
| Treatment protocol |
Cell suspensions were sprayed on glass or Parafilm; droplet size on Parafilm did not exceed 2 mm
|
| Growth protocol |
Ustilago maydis strains were grown to mid-log phase (OD600 of 0.8) in liquid YEPSL medium and resuspended in 2% YEPSL (OD600 of 1.0) supplemented with or without 100 uM 16-hydroxy hexadecanoic acid (HDA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested from the surfaces using a cell scraper and total RNA was extracted with Aquaphenol/Chloroform.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated aRNA was prepared from 100 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
15 ug of fragmented aRNA were hybridized on GeneChip UstilagoA custom arrays and washed with Affymetrix protocols (GeneChip Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)
|
| Scan protocol |
GeneChips were scanned using Affymetrix GSC3000G
|
| Description |
Gene expression data from U. maydis incubated for 12 on hydrophobic surface
|
| Data processing |
Data was analyzed with GCOS (Affymetrix Microarray Suite 5.9) to create CEL files. Data was normalized with the RMA method using Partek Genomics Suite 6.5
|
| |
|
| Submission date |
Jan 09, 2014 |
| Last update date |
Jul 23, 2014 |
| Contact name |
Regine Kahmann |
| E-mail(s) |
kahmann@mpi-marburg.mpg.de
|
| Organization name |
MPI for Terrestrial Microbiology
|
| Department |
Organismic Interactions
|
| Lab |
Kahmann
|
| Street address |
Karl-von-Frisch Str. 10
|
| City |
Marburg |
| ZIP/Postal code |
35043 |
| Country |
Germany |
| |
|
| Platform ID |
GPL3681 |
| Series (1) |
| GSE53947 |
Ustilago maydis gene expression after growth on hydrophobic surface plus/minus hydroxy fatty acids |
|
