|
| Status |
Public on Feb 27, 2010 |
| Title |
Dye swapped controlt2hvsCDt2h rep8 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Cadmium untreated cells and incubation for 2h
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
stress treatment: none (reference)
|
| 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
|
| |
|
| Channel 2 |
| Source name |
Cadmium treated cells and incubated for 2h
|
| Organism |
Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 |
| Characteristics |
stress treatment: D.radiodurans R1 exposed to 100 µM CdCl2 and incubated 2 h (test)
|
| 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
|
| |
|
| |
| Hybridization protocol |
The labeled cDNA pools were mixed, dried, and dissolved with hybridization buffer. The probes were denatured by heating and hybridized simultaneously to a prehybridized DNA microarray slide for 16 h at 42°C in a MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT, USA) with gentle mixing, After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Genepix Pro 4000B scanner.
Images were quantified using Genepix Pro Software (version 6.0).
|
| Description |
none
|
| Data processing |
LOWESS normalized, performed in GeneSpringGX 11 software, Agilent.
|
| |
|
| Submission date |
Feb 17, 2010 |
| Last update date |
Feb 26, 2010 |
| Contact name |
sun wook Jeong |
| E-mail(s) |
[email protected]
|
| Phone |
82-063-570-3146
|
| Organization name |
Korea atomic energy research institute
|
| Department |
Radiation biotechnology
|
| Lab |
Microbiology
|
| Street address |
Sinjeongdong 1266
|
| City |
chongup |
| State/province |
Chonbuk |
| ZIP/Postal code |
580-910 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL10060 |
| Series (1) |
| GSE20383 |
Transcriptional profiling of Deinococcus radiodurans comparing wild type cells with treated cells at four time points |
|
