|
| Status |
Public on May 31, 2015 |
| Title |
DMBQ_3h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
DMBQ-treated roots for 3 h (2nd Biological Replicate)
|
| Organism |
Phtheirospermum japonicum |
| Characteristics |
tissue: Root
treatment time-point (h): 3
age: 2 weeks old
|
| Treatment protocol |
2-week-old P. japonicum roots were covered with 7 ml solution of Haustorium-inducer 2,6-dimethoxy-p-benzoquinone (DMBQ) with 10 µM and kept horizontally covered with alluminium foil for 0, 0.5, 1, 3, 6, 12, 24 and 48 h. Mock samples were treated with solution with equal amount of DMSO, which was the solvent used to dissolve DMBQ chemical.
|
| Growth protocol |
Sterilized seed coat of Phtheirospermum japonicum was germinated in vitro after a vernalization period of 1 day at 4C (in darkness) and 2 days at 26C (darkness). Seedlings were kept growing vertically under photoperiod of 26C 16 h light/8 h dark for 2 weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using LiCl-based protocol as described in Ishida et al 2015
|
| Label |
Cyanine 3-labeling
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.25 µg RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) (5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent technologies, Santa Clara CA / US). 0.6 µg Cy3-labeled fragmented cRNA in hybridization buffer were hybridized overnight (65°C) to customized Oligo Microarrays 8x60K using Agilent's recommended hybridization chamber and oven. After hybridization, microarrays were washed with Agilent Gene Expression Wash Buffer 1 (1 min, room temperature) without agilation followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (1 min, 37°C) with agitation.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies)
|
| Description |
Design number of Microarray slide: 253261110001
|
| Data processing |
The Agilent Feature Extraction Software (v 10.7.3) was used to read out and process the microarray image files. Normalization of signal intensities from the single-experiment raw data lists were done in GeneSpring version 11 by dividing the intensity values by their median with percentage shift set as 75%.
|
| |
|
| Submission date |
Feb 06, 2015 |
| Last update date |
May 31, 2015 |
| Contact name |
Juliane Karine Ishida |
| E-mail(s) |
julianeishida@gmail.com
|
| Phone |
+81455039574
|
| Organization name |
RIKEN
|
| Department |
CSRS
|
| Lab |
Plant Immunity Research Group
|
| Street address |
1-7-22 Suehiro-cho, Tsurumi-ku
|
| City |
Yokohama |
| State/province |
Kanagawa |
| ZIP/Postal code |
230-0045 |
| Country |
Japan |
| |
|
| Platform ID |
GPL19750 |
| Series (1) |
| GSE65723 |
Root transcriptome of the facultative parasitic plant Phtheirospermum japonicum |
|
