Computational protocol: Ecrg4 peptide is the ligand of multiple scavenger receptors

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Protocol publication

[…] Total RNA was prepared as described above, amplified and labelled with cyanine 3 using the one-colour Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions. The labelled cRNA was fragmented and hybridised to the Agilent Whole Mouse Genome Microarray 4 × 44 K ver. 2.0. After the microarrays were washed, they were scanned with an Agilent DNA Microarray Scanner. The intensity value for each scanned feature was quantified with the Agilent Feature Extraction software, which subtracted the background. Agilent GeneSpring GX version 12.1 was used for normalisation, as follows. First, signal intensities <1.0 were set to 1.0. Each chip was then normalised to the 75th percentile of the measurements taken from that chip. Finally, the normalised intensities were log2-transformed. The microarray data have been submitted to the National Center for Biotechnology Information Gene Expression Omnibus (GEO) and are available under accession number GSE106400S. […]

Pipeline specifications

Software tools Agilent Feature Extraction, GeneSpring GX
Databases GEO
Application Gene expression microarray analysis
Organisms unidentified retrovirus
Chemicals Amino Acids