|
| Status |
Public on Feb 24, 2006 |
| Title |
before fermentation 2 |
| Sample type |
RNA |
| |
|
| Source name |
mRNA T128
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Typical commercial baker’s yeast used in Japan
|
| Treatment protocol |
Cell pellets (11,700 OD units) were suspended in 390 ml of LF medium in a 500-ml flask and then fermented at 30C for 300 min.To investigate gene expression profiles during initial stages of dough-fermentation, cell samples for DNA microarray analysis were obtained from each culture medium at 15 min, 30 min, and 60 min.(after_15min, after_30min, after_60min)
|
| Growth protocol |
Mini-scale fed-batch pre-cultivation was done using a jar fermentor (1-liter, B. E. Marubishi, Japan) and peristaltic pump (EYELA, Japan) with a sequential controller (B. E. Marubishi). After 18 h cultivation, cells in stationary phase were collected by centrifugation (2,700g for 5 min). Some of the cell pellets were suspended in 900 ml of sterilized water (4C). Cells for no-fermentation control were harvested after the fed-butch cultivation and stored at -80C until RNA extraction. (before_fermentation)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Each time samples of total RNA were extracted using the hot phenol method. Poly (A)+ RNA was isolated from the total RNA by using an Oligotex® dt30 (super) mRNA purification kit (Takara, Japan) according to the manufacturer’s instructions. Yeast genome arrays (YGS98 GeneChip®, Affymetrix, Santa Clara, CA) were used as DNA microarrays in this study.
|
| Label |
Biotin
|
| Label protocol |
Labeling was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual.
|
| |
|
| Hybridization protocol |
DNA microarray hybridization was done according to the Affymetrix GeneChip® Expression Analysis Technical Manual. In brief, hybridization was at 45C in a hybridization oven (model 640, Affymetrix) at 60 rpm for 16 h. The EukGE-WS2v4 fluidics protocol of the Affymetrix Microarray Suite Version 5.0 (MASv5.0) software was used to perform staining and washing procedures.
|
| Scan protocol |
The arrays were subsequently read using a GeneArray Scanner (Agilent technologies, Palo Alto, CA).
|
| Description |
before fermentation (replicate)
|
| Data processing |
Affymetrix Microarray Suite Version 5.0
|
| |
|
| Submission date |
Aug 01, 2005 |
| Last update date |
Feb 24, 2006 |
| Contact name |
Jun Shima |
| E-mail(s) |
shimaj@nfri.affrc.go.jp
|
| Organization name |
National Food Research Institute
|
| Department |
Applied Microbiology
|
| Lab |
Yeast
|
| Street address |
1-2-12 Kannondai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8642 |
| Country |
Japan |
| |
|
| Platform ID |
GPL90 |
| Series (1) |
| GSE3043 |
Functional Genomic Analysis of Commercial Baker’s Yeast during Initial Stages of Model Dough-Fermentation |
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