|
| Status |
Public on Dec 10, 2018 |
| Title |
C-LSER3-7DAF: Control Lateral Starchy Endosperm Replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
LSE Lateral Starchy Endosperm
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Koshihikar
tissue: Endosperm
developmental stage: Lateral Starchy Endosperm
|
| Treatment protocol |
Control and high temperature condition were set at 26/20 oC and 33/27 oC (day/night), respectively. Day and night length was 13 (0600-1900 h) and 11 (1900-0600 h) hours, respectively. Plants were kept in the chambers from three days after flowering until 30-35 DAF
|
| Growth protocol |
Rice plants cv. 'Koshihikari' were grown in 1/2000 pots. At three days after flowering (DAF), pots were moved to the naturally-illuminated temperature controlled chamber.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Developing caryopses was fixed with the ice-cooled mixture of ethanol-acetic acid (3 :1), embeded in 2% carboxymethyl cellulose following the method of Ishimaru et al. (2007). After making the cryo-section, fine tissues of developing endosperm were microdissected with AS LMD system (Leica Microsystems, Germany). Total RNA was extracted with Picopure RNA isolation kit (Arcturus Engineering).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (5.0 ng) was amplified to obtain complementary RNA (cRNA) using two-color Quick Amp Labeling kit (Agilent technologies). RNA extracted from control and high-temperature condition was labeled with cyanine-3 (Cy3)-CTP and cyanine-5 (Cy5)-CTP, respectively. Three biological replicates were prepared from high temperature conditions as well under control conditions.
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| |
|
| Hybridization protocol |
1250 ng of labeled cRNAs were fragmented and hydridized on a slide glass of rice 4 × 44K microarray RAP-DB (G2519F#1524 ; Agilent Technologies).
|
| Scan protocol |
Slides were scanned on an Agilent G2505B DNA microarray scanner, and background of the Cy3 and Cy5 raw signals was corrected using the Feature Exraction (ver. 10.5.1.1, Agilent Technologies).
|
| Description |
Raw data file: US22502560_251524110676_S01_GE2-v5_95_Feb07_1_4.txt
A microdissected samples of lateral starchy endosperm at 7DAF (days after fertilization) from control condition;Biological replicate 3 of 3.
|
| Data processing |
The two channels Agilent microarray expression data of 12 microdissected samples of dorsal aluerone cells (AL), dorsal starchy endosperm (DSE), central starchy endosperm (CSE) and lateral starchy endosperm (LSE) at 7DAF from control and at 6DAF from heat stressed tissues consisting of three replicates was further processed (ratio computation, log transformation and baseline transformation) using the software GeneSpring GX version 12 (Agilent, Santa Carla, CA).
Limma R (Ritchie et al., 2015) package is used following the empirical Bayes method (Smyth, 2004) to shrink the probe-wise sample variances towards a common value and to augmenting the degrees of freedom for the individual variances. The P-values adjustment method was used (Bonferroni, 1936). The top-ranked genes having an adjusted P-value below <=0.05 and log2 fold change above +/- 1 were selected.
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| |
|
| Submission date |
Nov 02, 2018 |
| Last update date |
Dec 10, 2018 |
| Contact name |
Tsutomu Ishimaru |
| E-mail(s) |
cropman@affrc.go.jp
|
| Organization name |
Central Region Agricultural Research Center, National Agriculture and Food Research Organization (CARC/NARO)
|
| Street address |
1-2-1 Inada, Joetsu, Niigata
|
| City |
Niigata |
| ZIP/Postal code |
941-0193 |
| Country |
Japan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE122115 |
Laser microdissection-based tissue specific transcriptome analyses reveals novel regulatory network of genes involved in heat-induced grain chalk in rice endosperm. |
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