8 protocols
Agilent One-Color Microarray-Based Gene Expression (Hybridization) Version: 5.7 Agilent publication number: G4140-90040 URL: http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_One-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 one-color gene expression analysis.
normalization data transformation protocol
Probe-level expression data were summarized into gene-level expression values by Tukey’s median polish algorithm according to Tukey, 1977 and Irizarry et al, 2003.
normalization data transformation protocol
Data was normalized by variance stabilizing normalization (VSN) using the normalizeVSN function in limma package of Bioconductor. The normalized expression values are log2 transformed.
array scanning protocol
Slides were scanned for single color at 5 µm resolution, 20 bits.
(Parameters: Scanning hardware = OTHER: Agilent Technologies Scanner G2505C, Scanning software = Feature Extraction Software [Agilent])
nucleic acid extraction protocol
Standard protocol recommended by the manufacturer (http://tools.invitrogen.com/content/sfs/manuals/Trizol_Plus_man.pdf)
(Parameters: Extracted product = total_RNA, Amplification = none)
treatment protocol
Dauers were filtered on a 8 µm pore-sized membrane and placed in a desiccation chamber equilibrated at 98% RH for 1 day. Each sample consists of thousands of nematodes being pooled into a single sample, and RNA was extracted from each pool.
growth protocol
daf-2 gravid hermaphrodites were bleached and the eggs were put into complete S-medium supplemented with E. coli NA22
(Parameters: start time = 5, time unit = days, min temperature = 25, temperature unit = C, media = Complete S-medium with E. coli NA22)