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| Status |
Public on Oct 14, 2014 |
| Title |
ZM4 (ATCC31821) treated by 220 g/L glucose for 2 hours rep-1 |
| Sample type |
RNA |
| |
|
| Source name |
ZM4 (ATCC31821)treated by 220 g/L glucose for 2 hours rep-1
|
| Organism |
Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 |
| Characteristics |
genotype: wild type
|
| Treatment protocol |
The fresh cultures were subcultured to the inoculum media with 5% of the inoculation and cultivated for 16 h at 30°C.Then the appropriate amount of glucose and sorbitol was added when the ZM4 reached the midexponential phase. The initial concentrations were nearly 0, 220 g/L of glucose, 220 g/L of glucose and 10mM of sorbitol. The time of taking samples was set at 6 hrs(0 g/L glucose), 8 hrs(220 g/L of glucose), 12 hrs(220 g/L of glucose and 10 mM of sorbitol), 20 hrs(220 g/L of glucose) after treatment, respectively.
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| Growth protocol |
Z. mobilis ZM4 (ATCC31821) was cultured in Rich Media (RM) at 30°C for 24-48 hours without shaking.Goodman AE, Rogers PL, Skotnicki ML. Appl Environ Microbiol. 1982, 44(2):496 –498.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Twelve samples representing four patterns of growth conditions in the exponential phase from ZM4 cultures were harvested by centrifugation and total cellular RNA was isolated using an RNA extraction kit (Kangwei century Biotech Co., Ltd., China).The remaining genomic DNA in the RNA samples was erased by following the manufacturer’s protocol (Takara Biotechnology (Dalian) Co., Ltd.). The RNA quality was evaluated by agarose gel electrophoresis and the ratio of its OD 260 to OD280 by a spectrophotometer, respectively.
|
| Label |
Cy3
|
| Label protocol |
The purified RNA from each sample was used as the template to generate cDNAs while labeled with Cy3-dUTP (CapitalBio).
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|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
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| 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 ZM4. It is the first of three wild-type biological replicates treated by 220 g/L glucose for 2 hours, each from separate cultures.
|
| Data processing |
Image signals were transformed into digital signals by NimbleScan 2.6 software and corrected by normalization method of RMA (Robust Multichip Analysis) to remove variations. It’s necessary to note that the group will be filtered if all digital signals of its four types for any gene were below 400 of cutoff. In a comparison analysis, the significant analysis of microarray software (SAM, version 3.02) was performed to identify significantly differentially expressed genes between treated and control groups.
Genes were determined to be significantly differentially expressed with a selection threshold of false discovery rate: FDR <5 % and fold change ≥2 (significant induction) or ≤0.5 (significant repression).
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| Submission date |
Aug 07, 2013 |
| Last update date |
Oct 15, 2014 |
| Contact name |
kun zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Sichuan University
|
| Department |
College of Life Sciences
|
| Lab |
Sichuan Key Laboratory of Molecular Biology and Biotechnology
|
| Street address |
section 29，Wangjiang Rd.
|
| City |
chengdu |
| State/province |
sichuan |
| ZIP/Postal code |
610064 |
| Country |
China |
| |
|
| Platform ID |
GPL17542 |
| Series (1) |
| GSE49620 |
Transcriptional analysis of adaptation to high glucose concentration in Zymomonas mobilis |
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