6 protocols
AccessionNameType
P-AGIL-29
image_acquisition
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.
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-1
hybridization
Agilent One-Color Microarray-Based Gene Expression (Quick Amp Labeling)
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-MTAB-25975
bioassay_data_transformation
Data analysis was performed by using GeneSpring GX 11.0 software. The original data was cleansing and normalized using the robust multichip average (RMA) algorithm consists in three steps: background correction, p75 normalization and expression calculation. Subsequent to logarithms transformation, baseline transformation of the data was performed using the median of control samples.
P-MTAB-25974
specified_biomaterial_action
A sample of 2.5 ml of peripheral venous blood was collected in a PaxGene tube in the first 24 hours following admission to the ICU or to the Respiratory Medicine Service. Samples were immediately stored at -80 degrees C until RNA extraction.
P-MTAB-25973
nucleic_acid_extraction
Total RNA was extracted from blood samples using the PAXgene Blood RNA System (PreAnalytix, Hombrechtikon, Switzerland). RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and quality confirmed by RNA Experion Bioanalyzer (BioRad, California USA) assay. Up to 1750 ng of each RNA sample was concentrated with the RNeasy MinElute Cleanup kit (QIAGEN, Hilden, Germany). RNA was eluted with 10 microliter of RNase-free H2O.
(Parameters: Extracted product = total_RNA, Amplification = none)