|
| Status |
Public on Jan 01, 2017 |
| Title |
WT vs fe-1 -1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
fe-1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedling
genotype/variation: fe-1
age: day 7 (ZT15)
treatment: nontreatment
|
| Treatment protocol |
Dex treatments were performed as described in Yamaguchi et al., (2005). Seedlings were submerged for 2h in 1 μM Dex.
|
| Growth protocol |
Plants were grown on MS medium supplemented with 1% sucrose at 22ºC under the LD conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions
|
| Label |
Cy5
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA and Cyanine-5 (Cy5) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
WT (L.er)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedling
genotype/variation: WT
age: day 7 (ZT15)
treatment: nontreatment
|
| Treatment protocol |
Dex treatments were performed as described in Yamaguchi et al., (2005). Seedlings were submerged for 2h in 1 μM Dex.
|
| Growth protocol |
Plants were grown on MS medium supplemented with 1% sucrose at 22ºC under the LD conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA and Cyanine-5 (Cy5) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
0.825ug of Cy3-labelled cRNA and 0.825ug of cRNA Cyanine-5 (Cy5) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Arabidopsis (V4) Gene Expression Microarry for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT and Red PMT is set to 100%).
|
| Description |
Biological replicate 1 of 2
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Dec 12, 2012 |
| Last update date |
Jan 01, 2017 |
| Contact name |
Mitsutomo Abe |
| E-mail(s) |
mabe@biol.s.u-tokyo.ac.jp
|
| Phone |
+81-3-5841-4466
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Biology
|
| Street address |
7-3-1 Hongo
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8654 |
| Country |
Japan |
| |
|
| Platform ID |
GPL9020 |
| Series (1) |
| GSE42862 |
Transcription profiling of A. thaliana L.er vs fe-1 |
|
