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| Status |
Public on Aug 15, 2020 |
| Title |
root tip region 1 after 48 h well-water, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
root tip region 1 after 48 h well-water
|
| Organism |
Glycine max |
| Characteristics |
cultivar: cv.Magellan
treatment group: well-watered controls
tissue: root tip
|
| Treatment protocol |
Seedlings with primary roots approximately 15 mm in length were transplanted against the interior surface of Plexiglas cylinders (14.5 cm diameter) filled with a 1:1 (v/v) mixture of vermiculite (no. 2A, Therm-ORock East Inc., New Eagle, PA, USA) and Turface (Profile Products LLC, Buffalo Grove, IL, USA) at water potentials of -0.1 MPa (well-watered treatment, moistened to the drip point) or -1.6 MPa (water-stressed treatment). Totally around 300 roots for each sample with three biological replicates were collected and the root tips were sectioned into regions 1–2 (water stressed) and 1–3 (well-watered controls) after 5h and 48h respectively. The root samples were immediately frozen with liquid nitrogen and then stored at −80 °C.
|
| Growth protocol |
Soybean (cv.Magellan) seeds were surface sterilized in 1% NaClO solution for 2 min, rinsed in deionized water for 30 min and germinated between sheets of germination paper moistened with a solution containing 5 mm CaCl2 and 5 mm Ca(NO3)2 for 36 h at 29 °C and near-saturation humidity in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the root tissues using TRIZOL reagent (Invitrogen, Carlsbad, CA, USA). Genomic DNA was eliminated by digesting the RNA with Turbo DNA-free DNaseI (Ambion) according to the manufacturer’s instructions. After DNaseI treatment, RNA concentration was determined and checked the quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Total RNA was used for Affymetrix Soybean Genome GeneChip analysis following the manufacturer's recommended protocols (Affymetrix, CA). The cDNA synthesis, cRNA amplification, and synthesis of sense strand cDNAs were carried out using the Ambion WT expression kit.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
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| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
The arrays were scanned with a GeneChip 7G Plus high-resolution scanner.
|
| Description |
Gene expression data from soybean root tip well-water
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
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| |
|
| Submission date |
Aug 16, 2017 |
| Last update date |
Aug 15, 2020 |
| Contact name |
Babu Valliyodan |
| E-mail(s) |
valliyodanb@missouri.edu
|
| Phone |
5738846313
|
| Organization name |
University of Missouri
|
| Department |
Plant Sciences
|
| Lab |
Nguyen laboratory
|
| Street address |
1-31 Ag Building
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65201 |
| Country |
USA |
| |
|
| Platform ID |
GPL4592 |
| Series (1) |
| GSE102749 |
Gene expression of soybean root tips under water deficits |
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