|
| Status |
Public on Jul 07, 2014 |
| Title |
R1 vs. bphPR deletion |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
R1
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
genotype/variation: control
|
| Treatment protocol |
Non treatment
|
| Growth protocol |
R1 and bphPR deletion mutant cells were cultured O.D 1.0 at the 37 °C shaking incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
50 µg of total RNA were primed with 2 µl of 3 µg/µl random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 µl of 50X aminoallyl-dNTP mix, 25 µM Cy3-labeling dye and Cy5-labeling dye.
|
| |
|
| Channel 2 |
| Source name |
∆bphPR
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
genotype/variation: bphPR deletion mutant
|
| Treatment protocol |
Non treatment
|
| Growth protocol |
R1 and bphPR deletion mutant cells were cultured O.D 1.0 at the 37 °C shaking incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
50 µg of total RNA were primed with 2 µl of 3 µg/µl random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 µl of 50X aminoallyl-dNTP mix, 25 µM Cy3-labeling dye and Cy5-labeling dye.
|
| |
|
| |
| Hybridization protocol |
The hybridizations were conducted at 57°C for 17 hours in an Agilent Hybridization oven and washed following the manufacturer’s protocol (Agilent Technologies, Inc.).
|
| Scan protocol |
The scans were performed with an Agilent DNA microarray Scanner (Agilent Technologies, Inc.) using Agilent Feature Extraction software 10.7 (Agilent Technologies, Inc.). The signal intensities were quantified using GeneSpringGX 7.3.1 software (Agilent Technologies, Inc.).
|
| Data processing |
The normalization of gene expression by a LOWESS regression was applied for 3 data obtained from 3 biological replicates. The genes were considered to be differentially expressed when the logarithmic gene expression ratios had more than a 2-fold difference in the expression level.
The statistical significance of the data was determined by Student’s t test. P-values of less than 0.05 were taken to be statistically significant.
|
| |
|
| Submission date |
Jul 07, 2014 |
| Last update date |
Jul 07, 2014 |
| Contact name |
Im Seong Hun |
| E-mail(s) |
[email protected]
|
| Organization name |
Korea Atomic Energy Research Institute
|
| Street address |
Jeongeup 580-185, Republic of KoreaInstitute
|
| City |
Jeongeup |
| ZIP/Postal code |
580-185 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18898 |
| Series (2) |
| GSE59135 |
Deinococcus radiodurans R1 Cells: Control vs. bphPR deletion mutant |
| GSE59139 |
Mutation of bphP/bphR Decreases the Resistance of D. radiodurans to DNA-damaging Agents |
|
