|
| Status |
Public on Nov 05, 2021 |
| Title |
Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
7065.D1.L1.G.4C.B1
|
| Organism |
Saccharum officinarum |
| Characteristics |
tissue: leaves
variety: IACSP 97-7065 drought susceptible
|
| Treatment protocol |
7065: IACSP 97-7065 plants; D1: Droghut; L1: leaf+1; 4C: collection 4 (10 months of growth); B2: biological replicate 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction from leaves and internodes were performed using the protocol described by LOGEMANN, J. et al. Analytical Biochemistry, v. 163, p. 16-20, 1987. The RNA samples were treated with DNase in solution and purified on-column using the RNase-Free DNase Set (Qiagen, Hilden, Germany), according to the manufacturer.
|
| Label |
cy3
|
| Label protocol |
CyScribe Post-Labelling Kit Protocol - GE Healthcare
|
| |
|
| Channel 2 |
| Source name |
7065.I1.L1.G.4C.B1
|
| Organism |
Saccharum officinarum |
| Characteristics |
tissue: leaves
variety: IACSP 97-7065 drought susceptible
|
| Treatment protocol |
7065: IACSP 97-7065 plants; D1: Droghut; L1: leaf+1; 4C: collection 4 (10 months of growth); B2: biological replicate 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction from leaves and internodes were performed using the protocol described by LOGEMANN, J. et al. Analytical Biochemistry, v. 163, p. 16-20, 1987. The RNA samples were treated with DNase in solution and purified on-column using the RNase-Free DNase Set (Qiagen, Hilden, Germany), according to the manufacturer.
|
| Label |
cy5
|
| Label protocol |
CyScribe Post-Labelling Kit Protocol - GE Healthcare
|
| |
|
| |
| Hybridization protocol |
Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings
|
| Description |
Drought 10 months (irrigated as control) - Leaf +1 - Variety IACSP 97-7065 (susceptible)
|
| Data processing |
Feature Extraction 9.5.3.1 software (Agilent Technologies) was used to extract data using as reference the benchmark for Two-Color microarray from Agilent—February 2007 version (protocol GE2-v5_95_Feb07) with minor adjustments. After background signal correction, we conducted the normalization across the entire range of array data (a linear normalization method). LOWESS normalization was used to correct the intensity-dependent dye biases. Then, the outlier genes were identified using the HTself method (with minor adjustments) adapted for the Agilent Platform with 90% confidence.
|
| |
|
| Submission date |
Nov 03, 2021 |
| Last update date |
Nov 06, 2021 |
| Contact name |
Danyel Contiliani |
| E-mail(s) |
danyel.contiliani@usp.br
|
| Organization name |
University of Sao Paulo
|
| Street address |
Av. Bandeirantes, 3900
|
| City |
Ribeirão Preto |
| ZIP/Postal code |
14040-901 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL22278 |
| Series (1) |
| GSE187416 |
Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions |
|
