8 protocols
AccessionNameType
P-AGIL-2
hybridization
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.
P-AGIL-28
labeling
P-AGIL-28
P-MTAB-32802
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.
P-MTAB-32801
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.
P-MTAB-32800
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])
P-MTAB-32799
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)
P-MTAB-32798
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.
P-MTAB-32803
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)