|
| Status |
Public on May 15, 2019 |
| Title |
T. salsuginea, 72h low-oxygen treatment |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
root samples of A. thaliana under normal condition
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: normal condition
tissue: root
|
| Treatment protocol |
Two-week-old Arabidopsis or three-week-old closely related species were transferred into an airtight vacuum chamber in an environmentally controlled growth cabinet. The low-oxygen gas mixture (0.1% O2/99.9% N2) was supplied continuously into the airtight vacuum chamber to retain low O2 conditions during treatment.
|
| Growth protocol |
The plants were grown for 2~3 weeeks in an environmentally controlled growth chamber at 23℃ under constant light (approximately 100 µmol m-2s-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.
|
| Label |
Cy5,Cy3
|
| Label protocol |
Total RNA (5 ug) from root samples was reverse transcribed using reverse transcription (RT) primer tagged with either Cy3-3DNA or Cy5-3DNA capture sequence of Array 900 MPX Expression Array Detection Kits (Genisphere, Hatfield, PA, USA).
|
| |
|
| Channel 2 |
| Source name |
root samples of T. salsuginea exposed for 72 h to low-oxygen
|
| Organism |
Eutrema salsugineum |
| Characteristics |
treatment: 72 h to low-oxygen
tissue: root
|
| Treatment protocol |
Two-week-old Arabidopsis or three-week-old closely related species were transferred into an airtight vacuum chamber in an environmentally controlled growth cabinet. The low-oxygen gas mixture (0.1% O2/99.9% N2) was supplied continuously into the airtight vacuum chamber to retain low O2 conditions during treatment.
|
| Growth protocol |
The plants were grown for 2~3 weeeks in an environmentally controlled growth chamber at 23℃ under constant light (approximately 100 µmol m-2s-1).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany), following the manufacturer's instructions.
|
| Label |
Cy5,Cy3
|
| Label protocol |
Total RNA (5 ug) from root samples was reverse transcribed using reverse transcription (RT) primer tagged with either Cy3-3DNA or Cy5-3DNA capture sequence of Array 900 MPX Expression Array Detection Kits (Genisphere, Hatfield, PA, USA).
|
| |
|
| |
| Hybridization protocol |
The labeled cDNA was hybridized on Operon Arabidopsis Version 3.0 microarray which consists of 26,173 probes spotted with synthetic 70-mer oligonucleotides on aminosilane-coated slides by the David Galbraith lab, University of Arizona.
|
| Scan protocol |
The slides were scanned using an ArrayWoRx (Applied Precision, Issaquah, WA, USA).
|
| Description |
Analysis used RNA of A.thaliana under normal condition as control samples for comparison to the experimental samples(Brassicaceae species under low-oxygen treatment).
|
| Data processing |
Intensity values were quantified from the pairs of TIFF image files from each channel using version 5.6 ImaGene software (BioDiscovery, Los Angeles, CA, USA). The mean values from each channel were log2 transformed and normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from experimental with all replicates combined.
|
| |
|
| Submission date |
Apr 08, 2019 |
| Last update date |
May 16, 2019 |
| Contact name |
JiHye Hwang |
| E-mail(s) |
hwangjh0012@naver.com
|
| Organization name |
Ewha Womans University
|
| Street address |
52, Ewhayeodae-gil
|
| City |
Seoul |
| ZIP/Postal code |
03760 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26403 |
| Series (1) |
| GSE129468 |
Low-oxygen stress responses of Brassicaceae Species |
|
