|
| Status |
Public on Jan 06, 2015 |
| Title |
trm2_41_0min_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
trm2 cells, 41 ℃, 0 minute, replicate 1
|
| Organism |
Corynebacterium glutamicum |
| Characteristics |
strain: trm2
sampling time: 0 minute
|
| Treatment protocol |
When OD610 of the cultures reached around 7, the growth temperature increased to 41 ℃, and the cultures were incubated for additional 1 hour.
|
| Growth protocol |
All strains were grown in 10 ml A medium supplemented with 4 % glucose at 33 ℃ with agitation (200 rpm).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extacted from each sample with NucleoSpin RNA (TaKaRa Bio Inc., JAPAN), according to the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) using the SuperScript Indirect cDNA Labeling system (Life Technologies).
|
| |
|
| Hybridization protocol |
Hybridization was performed using Gene Expression Hybridization Kit according to the manufacture’s manual (Agilent). The labeled cDNA was hybridized to microarrays in an Agilent Technologies Microarray chamber at 65˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), and 1 minute with 37˚C GE Wash buffer 2 (Agilent).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm using single color scan setting for 4x44k array slides. PMT is set to 100% for Cy3 channels.
|
| Description |
gene expression 0 minute after growth temperature upshift
|
| Data processing |
The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE1_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile).
|
| |
|
| Submission date |
Jan 05, 2015 |
| Last update date |
Jan 06, 2015 |
| Contact name |
Shinichi Oide |
| E-mail(s) |
soide@rite.or.jp
|
| Organization name |
Research institute of Innovative Technology for the Earth (RITE)
|
| Street address |
9-2 Kizugawadai, Kizugawa
|
| City |
Kyoto |
| ZIP/Postal code |
619-0292 |
| Country |
Japan |
| |
|
| Platform ID |
GPL17881 |
| Series (1) |
| GSE64654 |
Transcriptome analyses of the Corynebacterium glutamicum strains adapted to supraoptimal growth temperatures |
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