|
| Status |
Public on Oct 07, 2016 |
| Title |
Shoot apices, Triple mound, Bowman, replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Immature shoot apices, WT, triple mound
|
| Organism |
Hordeum vulgare |
| Characteristics |
cultivar/background: Bowman
genotype/variation: Wild type
developmental stage: Triple mound
tissue: Immature shoot apices
|
| Treatment protocol |
The seeds were initially germinated in 96-well planting trays under long day conditions, with 16 h light/8 h dark and a temperature of 20±2ºC during the day and 16±2 ºC during the night for 14 days. After 14 days, the plants were vernalized for four weeks at 4˚C. The vernalized plants were hardened for 2 weeks (12/12 h (day/night) and temperature 12±2ºC).
|
| Growth protocol |
The five vrs2 mutants were obtained from USDA, ARS, USA, Nordic genetic resources center, Sweden and IPK Genebank, Germany. The Bowman near isogenic line of vrs2.e, BW-NIL(vrs2.e), was crossed with Bowman and Golden Promise to generate F2 mapping populations (Bowman × BW-NIL(vrs2.e) and Golden Promise × BW-NIL(vrs2.e)). All plant materials used in this study were grown under greenhouse conditions. The immature shoot apices collected from BW-NIL(vrs2.e) and WT progenitor Bowman at TM, GP, SP, and AP were used for RNA extraction.
|
| 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 |
The RNA was labeled through the application of a Low Input QuickAmp Labeling kit (Agilent Technologies). The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen).
|
| |
|
| 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 |
Agilent G5761A SureScan Dx.
|
| Description |
Gene expression from immature shoot apices at Triple mound stage of wild type.
|
| Data processing |
GeneSpring 12.0.
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 |
Oct 06, 2016 |
| Last update date |
Oct 07, 2016 |
| Contact name |
Dr.Nese Sreenivasulu |
| E-mail(s) |
[email protected]
|
| Phone |
+63(2)580-5600
|
| Organization name |
IRRI
|
| Street address |
Metro Manila
|
| City |
Los Banos |
| ZIP/Postal code |
7777 |
| Country |
Philippines |
| |
|
| Platform ID |
GPL22533 |
| Series (1) |
| GSE87731 |
VRS2 regulates hormone-mediated inflorescence patterning in barley |
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