6 protocols
Agilent G2565AA and G2565BA Microarray Scanner and Feature ExtractionVersion: 7.0,10.5Agilent publication number: G2566-90017, G4460-90019URL: http://www.chem.agilent.com/Library/usermanuals/Public/G2566-90017.pdf, http://www.chem.agilent.com/Library/usermanuals/Public/G4460-90019_FE_10.5_User.pdfScanner manual for software release 7.0. The Feature Extraction Software User Guide shows you how to set up and run Feature Extraction automatically for a batch of image files and how to extract image files in real time.
nucleic acid hybridization to array protocol
Overall 25,262 transcripts were represented on the microarray by 1, 2 or 3 individual probes. Hybridizations for all experimental conditions were performed in 4 replicates. Total RNA samples derived from the treatments were hybridized against the pooled control respective to their origin. The microarray hybridization procedure was carried out with 300ng of cyanine-3 and cyanine-5 labelled cRNA for 17h at 65°C. Control/control hybridization were performed, each component of the pooled control (LP 2°C, LP 7°C, LP 12°C) was hybridized against the pooled control to mitigate dye bias effects. Subsequently microarray disassembly and wash procedure followed as described by the manufacturer’s instructions (Agilent).
Agilent Two-Color Microarray-Based Gene Expression (Quick Amp Labeling)
Version: 5.7
Agilent publication number: G4140-90050
URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90050_Two-Color_GE_5.7.pdf
This document describes Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for microarray-based two-color gene expression analysis.
The growth conditions of the plants are as follows: The plants were grown in the plastic dishes containing MS medium. MS medium contained Murashige and Skoog salts, 1% sucrose (WAKO, Osaka, Japan) and 0.9% Bacto-agar (Difco, Detroit, MI, USA). The plants were grown for 10 days in a growth chamber at 22C and 50-60% humidity under 16 hr light/8 hr dark.
(Parameters: start time = 10, time unit = days, min temperature = 22, temperature unit = C)
Plants were grow on the MS medium plate containing 0.5 uM ABA for 10 days. The plants were harvested, immediately frozen by liquid nitrogen and stored at a deep freezer.
Total RNAs were isolated using the RNAiso Reagent (Takara, Japan).
(Parameters: Extracted product = total_RNA, Amplification = none)