|
| Status |
Public on Jul 31, 2018 |
| Title |
the sigD mutant1 at the exponential phase_1st [Agilent-025748] |
| Sample type |
RNA |
| |
|
| Source name |
sigD mutant_exponential phase
|
| Organism |
Corynebacterium glutamicum R |
| Characteristics |
genotype/variation: sigD deletant
growth phase: exponential phase
|
| Growth protocol |
C. glutamicum strains are grown in 100 ml of nutrient rich A medium containing 1% glucose in 500 ml flask at 33˚C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from C. glutamicum cells using NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacture's manual.
|
| 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 |
sigD_1st
|
| 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 13.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended Percentile shift normalization (50th percentile) and baseilne was transformed to median of all samples.
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| |
|
| Submission date |
Aug 07, 2017 |
| Last update date |
Jul 31, 2018 |
| Contact name |
Masayuki Inui |
| E-mail(s) |
mmg-lab@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 |
GPL20865 |
| Series (2) |
| GSE102328 |
Transcriptome analysis of the sigD deletion mutant using the Agilent platform arrray [Agilent-025748] |
| GSE102329 |
Genome-wide analyses of C. glutamicum SigD |
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