|
| Status |
Public on Dec 18, 2013 |
| Title |
Haloferax mediterranei ΔdeoR2 with induction by fructose vs without induction replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ΔdeoR2_induced by fructose
|
| Organism |
Haloferax mediterranei |
| Characteristics |
strain: DF50
genotype/variation: ΔdeoR2
induced by: fructose (at final conc. 50mM)
|
| Treatment protocol |
fructose (soluted in TBSL buffer) was added into the culture to a final concentration of 50mM, and a same volume TBSL buffer was added into the other culture, both two were incubated for 45 before harvested.
|
| Growth protocol |
Cells of H. mediterranei DF50 or DF50 delta deoR2 were grown at 37°C until OD600 reached 1.5 in AS-168SYL medium,
|
| 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 |
ΔdeoR2_control
|
| Organism |
Haloferax mediterranei |
| Characteristics |
strain: DF50
genotype/variation: ΔdeoR2
sample type: control (no induction)
|
| Treatment protocol |
fructose (soluted in TBSL buffer) was added into the culture to a final concentration of 50mM, and a same volume TBSL buffer was added into the other culture, both two were incubated for 45 before harvested.
|
| Growth protocol |
Cells of H. mediterranei DF50 or DF50 delta deoR2 were grown at 37°C until OD600 reached 1.5 in AS-168SYL medium,
|
| 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 |
Agilent G2565C
|
| Description |
compare gene expression profiles of strain DF50 delta deoR2 under the induction by fructose
|
| 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, lowess normalized log2 ratio (test/control) was calculated.
|
| |
|
| Submission date |
Sep 25, 2012 |
| Last update date |
Dec 20, 2013 |
| Contact name |
Lei Cai |
| Organization name |
Institute of Microbiology, Chinese Academy of Sciences
|
| Street address |
No.1 Beichen West Road, Chaoyang District,
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL16102 |
| Series (1) |
| GSE41134 |
Genes differentially expressed in Haloferax mediterranei strains, DF50 and ΔdeoR2, with or without induction by fructose |
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