|
| Status |
Public on Apr 20, 2012 |
| Title |
control wild-type strain vs ΔphaEC strain replicate 6 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
wild-type strain
|
| Organism |
Haloferax mediterranei |
| Characteristics |
Stage: late exponential
strain: wild-type
|
| Treatment protocol |
The wild-type strain and ΔphaEC strain were harvested at the late exponential stage.
|
| Growth protocol |
The wild-type strain and ΔphaEC strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.
|
| |
|
| Channel 2 |
| Source name |
ΔphaEC strain
|
| Organism |
Haloferax mediterranei |
| Characteristics |
Stage: late exponential
strain: ΔphaEC
|
| Treatment protocol |
The wild-type strain and ΔphaEC strain were harvested at the late exponential stage.
|
| Growth protocol |
The wild-type strain and ΔphaEC strain were were cultivated at 37°C to late exponential growth phase in MG medium containing 10 g/L glucose as carbon source.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol (invitrogen) following manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.
|
| |
|
| |
| Hybridization protocol |
standard CapitalBio Methods
|
| Scan protocol |
Luxscan 10K (CapitalBio)
|
| Description |
compare gene expression profiles of wild-type strain with ΔphaEC strain
|
| Data processing |
After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed. For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy,the geometric mean of lowess normalized log2 ratio (test/control) of two dye-swap slides was calculated. SAM (significance Analysis of Microarrays, version 2.23b) software was used to normalize data.
|
| |
|
| Submission date |
Apr 19, 2012 |
| Last update date |
Apr 20, 2012 |
| Contact name |
Jing Han |
| E-mail(s) |
hanjing@im.ac.cn
|
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
|
| Street address |
NO.1 West Beichen Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL15465 |
| Series (1) |
| GSE37421 |
Genes differentially expressed Haloferax mediterranei strains: control wild-type strain vs ΔphaEC strain |
|
