|
| Status |
Public on Dec 01, 2016 |
| Title |
bdf1Δ vs W303 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
bdf1∆ under salt treatment
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: bdf1{delta}
stress: salt
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total yeast RNA was isolated using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany).
|
| Label |
Cy5
|
| Label protocol |
Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Bio-Sciences, Piscataway, NJ, USA) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. The total RNA was purified using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany). Because oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.
|
| |
|
| Channel 2 |
| Source name |
W303 under salt treatment
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: W303
stress: salt
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total yeast RNA was isolated using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany).
|
| Label |
Cy3
|
| Label protocol |
Fluorescent dye (Cy5 and Cy3-dCTP, GE Healthcare Bio-Sciences, Piscataway, NJ, USA) labeled DNA was produced through Eberwine's linear RNA amplification method.and subsequent enzymatic reaction. The total RNA was purified using NucleoSpin® RNA clean-up kits (MACHEREY-NAGEL, Germany). Because oligonucleotide arrays were used here, we took a cDNA labeling approach with Klenow enzyme after reverse transcription.
|
| |
|
| |
| Hybridization protocol |
Labeled control and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and mixed into 80uL hybridization solution (3×SSC, 0.2%SDS, 5×Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min before loading onto a microarray. The array was hybridized at 42°C overnight and washed with two consecutive washing solutions (0.2% SDS，2×SSC at 42°C for 5 min, and 0.2×SSC for 5 min at room temperature).
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a LuxScan3.0 fluorescent scanner (Capital Bio Corp. Beijing, China), and image intensity data were extracted and analyzed with a GenePix Pro 4.0 (Axon Instruments, Foster City, CA).
|
| Description |
For each test and control sample, two hybridizations were performed by using a reversal fluorescent strategy. Only genes whose alteration tendency kept consistency ( > 2-fold) in both microarray were selected as differentially expressed genes
|
| Data processing |
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. Only genes whose alteration tendency kept consistency (both above 2-fold) in both microarray were selected as differentially expressed genes.
|
| |
|
| Submission date |
Dec 09, 2015 |
| Last update date |
Dec 01, 2016 |
| Contact name |
Xiaoming Bao |
| E-mail(s) |
bxm@sdu.edu.cn
|
| Phone |
(86) 053188365826
|
| Organization name |
Shandong University
|
| Department |
State Key Laboratory of Microbial Technology
|
| Lab |
Bao lab
|
| Street address |
Shanda Nan Road 27
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250100 |
| Country |
China |
| |
|
| Platform ID |
GPL17201 |
| Series (1) |
| GSE75828 |
HAL2 overexpression induces iron acquisition and enhanced salt resistance in bdf1Δ |
|
