|
| Status |
Public on Jul 28, 2017 |
| Title |
GTC_48hr_LP104_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Germinating barley seeds, LP104, 48hr, replicate 3
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: Germinating seeds
line: LP104
|
| Growth protocol |
grains were germinating for 0-144 hours in the dark at 14.5°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tissues using the Plant Mini RNA kit (Qiagen, Hilden, Germany) following the manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600ng of Cy3-labeled, amplified cRNA were hybridized, following the manufacturer's protocol, to a custom-synthesized 60k Barley Microarray (Agilent Technologies)
|
| Scan protocol |
Scanning of the slides was performed at high resolution of 3 µm double pass using Agilent DNA Microarray Scanner G2565CA
|
| Description |
Gene expression 48 hours after imbibition
|
| Data processing |
The scanned images were analyzed with GeneSpring 12.0 software. After doing quantile normalization and baseline transformation to median of all samples, the probe sets (genes) were filtered by Coefficient of Variation <50%, followed by Moderated T-Test and Bonferroni correction. The probe sets which passed the P value cut-off ≤0.01 with the fold change of ≥2.0 were considered for interpreting the data
|
| |
|
| Submission date |
Jul 27, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Andreas Graner |
| E-mail(s) |
[email protected]
|
| Phone |
+49 394 825 220
|
| Organization name |
Leibniz Institute of Plant Genetics and Crop Plant Research
|
| Street address |
Corrensstrasse 3
|
| City |
Gatersleben |
| ZIP/Postal code |
06466 |
| Country |
Germany |
| |
|
| Platform ID |
GPL22533 |
| Series (1) |
| GSE101962 |
Gene expression analysis of two elite breeding barley lines with distinct tolerance to abiotic stress |
|
