|
| Status |
Public on Jul 15, 2014 |
| Title |
wt_3rd |
| Sample type |
RNA |
| |
|
| Source name |
wild-type strain
|
| Organism |
Corynebacterium glutamicum R |
| Characteristics |
background strain: R
genotype: wild type
|
| Growth protocol |
C. glutamicum R wild-type and gntR1 deleted cells were grown aerobically in nutrient-rich A medium supplemented with 2% (w/v) glucose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from exponentially-growing cells (OD610 of 2.0) using the Nucleo Spin RNA (MACHEREY-NAGEL).
|
| 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.
|
| 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 |
Jun 18, 2014 |
| Last update date |
Jul 15, 2014 |
| Contact name |
Norihiko Takemoto |
| E-mail(s) |
ntakemoto@ri.ncgm.go.jp
|
| Organization name |
Research Institute of National Center for Global Health and Medicine
|
| Lab |
Pathogenic Microbe Laboratory
|
| Street address |
1-21-1, Toyama
|
| City |
Shinjuku-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
162-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18839 |
| Series (2) |
| GSE58631 |
WT vs gntR1 mutant gene expression profiles |
| GSE58633 |
gntR1 mutant gene expression profiles and Chip-chip analysis of GntR1 |
|
