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Pipeline publication

[…] e tags []. All sequence data are available in the GEO Database under accession number GSE48036., To determine gene expression by microarray analysis, A549 cells were left untransfected or transfected with miRNA specific mimics as described above. Fifteen hours after transfection, cells were either mock infected or infected with A/WSN/33 (5 pfu/cell) for ten hours prior to RNA purification. Gene expression was measured by whole-genome microarray using an Illumina bead array in biological triplicate. Total RNA from three biological replicates was purified 10 hours post infection and hybridized to Illumina Bead Array whole genome expression microarray []. Microarray data was analyzed using the Limma software package in R Biocunductor. Samples were normalized by quantile normalization and gene expression differences were determined with a threshold of 1.5 fold change with a p-value of <0.05. Gene expression data are available in the GEO database under accession number GSE47937. Pathway analysis and GO term identification was performed with InnateDB [,]. Interactome analysis was generated using Cytoscape with the Agilent Literature Search plug-in []. MicroRNA seed match identification was performed using the TargetScan algorithm [] and the MiRWalk database []., To prepare whole cell extracts, A549 cells were washed in ice-cold phosphate buffered saline. Cells were then lysed as in [] and 10µg of total protein were separated by SDS-Page, transferred to nitrocellulose membrane, and then probed with specific antisera for HDAC1 and GAPDH (Santa Cruz Biotechnologies). Corresponding secondary antibodies conjugated to horseradish peroxidase (Calbiochem) were used. Antibody detection was visualized by chemiluminescence (PerkinElmer) using Vision Works software (UVP). Densitometry analysis was performed by comparing ratios of intensity of HDAC1:GAPDH for each sample using Vision Works software., To chara […]

Pipeline specifications

Software tools limma, Cytoscape, TargetScan
Databases miRWalk InnateDB