strain: wild type F verticillioides M3125 fumonisin producer: yes time: 48 hr
Growth protocol
F verticillioides was grown in liquid fumonisin media (GYAM) for 1, 2, 3 and 4 days, shaking at 250 rpm at 27C following Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249.
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).
Label
Cy3
Label protocol
Labeling was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.
Hybridization protocol
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.
Scan protocol
Scanning was performed by NimbleGen Systems Inc., Madison, WI, USA, following their standard operating protocol. See www.nimblegen.com.
Description
This sample is of wild-type Fusarium verticillioides M3125. It is the first of three biological replicates used in this experiment, each from separate cultures.
Data processing
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
