Computational protocol: Significant role of μ-calpain (CANP1) in proliferation/survival of bovine skeletal muscle satellite cells

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Protocol publication

[…] The total RNA was extracted from the transfected cells for microarray analysis. The synthesis of target cRNA probes and hybridization were performed using Agilent’s LowInput QuickAmp Labeling Kit (Agilent Technology, Santa Clara, CA) according to the manufacturer’s instructions. The fragmented cRNA was then re-suspended with 2× hybridization buffer and directly pipetted onto assembled bovine (V2) gene expression 4 × 44K microarray (Agilent Technologies). The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology), and the data quantification was performed using Agilent Feature Extraction software 10.7 (Agilent Technology). All data normalization and selection (fold-changed) were performed using GeneSpringGX 7.3.1 (Agilent Technology). Reliable genes were filtered by flag, following the Agilent manual. The average of normalized ratio was calculated by dividing the average of control normalized signal intensity by the average of test normalized signal intensity. Functional categorization of gene families over-represented was performed using the program from the NIAID web site (http://david.abcc.ncifcrf.gov/summary.jsp). […]

Pipeline specifications

Software tools Agilent Feature Extraction, DAVID
Application Gene expression microarray analysis
Organisms Bos taurus
Chemicals Cysteine