|
| Status |
Public on Jul 20, 2016 |
| Title |
6Day_Seedling_tt8-3_Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Whole seedling, 6 day old, tt8-3, replicate 1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Whole seedling
genotype/variation: tt8-3 mutant
|
| Growth protocol |
Arabidopsis seeds were surface sterilized using 30% Clorox with seven minutes incubation. This was followed by 6 times washing with autoclaved water.
Seeds were then placed on full strength MS media with 5% sucrose and 5% Phytoagar® for 4 days before placing them in growth chamber at 22°C for 16 hr light/8 hr dark cycle with relative humidity of 60-70 and illumination 70wm-2. Seedlings were harvested 6 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Omega® plant RNA extraction kit (Omega BIO-TEK) following manufacturer's guidelines. RNA was purified using an RNeasy purification kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
100 ng of total RNA was labeled with Low Input Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) following manufacturer instruction (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling, version 6.5). Briefly, 100 ng of total RNA was converted into double-stranded cDNA by priming with an oligo-dT primer containing the recognition site for T7 RNA polymerase. In vitro transcription with T7 RNA polymerase was used to produce cyanine 3-CTP labeled cRNA.
|
| |
|
| Hybridization protocol |
1.65µg of labeled cRNA was hybridized onto Agilent SurePrint G2 Agilent Arabidopsis V4 (4x44K) for 17 hours at 65oC, 10 rpm in Agilent hybridization oven. After hybridization, the microarray slide was washed in gene expression wash buffer 1 for one minute at room temperature and another minute in gene expression wash buffer 2 at 37 C. Hybridization: Gene Expression Hybridization Kit (Agilent: 5188-5242), Wash buffer: Gene Expression Wash Buffer Kit (Agilent: 5188-5327)
|
| Scan protocol |
Scanning was performed using on Agilent High Resolution Microarray Scanner (C-model)
|
| Description |
Gene expression in tt8-3
tt8-3_1_1 [10165]
|
| Data processing |
Raw signal data were extracted from the TIFF image with Agilent Feature Extraction Software (V10.7.1.1)
Normalization method: All probes were normalized using percentile shift to 75% and were baseline corrected to the median.
Software: Agilent GeneSpring
|
| |
|
| Submission date |
Jul 03, 2014 |
| Last update date |
Jul 20, 2016 |
| Contact name |
Sanjay Swarup |
| Organization name |
National University of Singapore
|
| Department |
Department of Biological Sciences
|
| Lab |
Metabolites Biology Lab
|
| Street address |
14 Science Drive 4
|
| City |
Singapore |
| ZIP/Postal code |
117543 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE59048 |
Coordinate Regulation of Metabolites Glycosylation and Stress Hormones Biosynthesis by TT8 in Arabidopsis |
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