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Protocol publication

[…] checked for RNA integrity using a Biorad Experion electrophoresis station (Biorad, Nazareth, Belgium) and analyzed on Sentrix Human-6 v2 Expression BeadChips from Illumina (San Diego, CA, USA) at the Finnish Microarray Centre (Turku, Finland) using protocols recommended by the manufacturer. Raw microarray data is available at Gene Expression Omnibus (GEO) under accession number GSE27270 (SubSeries of GSE27438). Microarray data analysis was performed using R statistical software version 2.11 (R Dev Core) with associated libraries from Bioconductor project version 2.6 (). Data was normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the lumi package (). Probe sets that were not linked to any known or predicted human gene were filtered out. Linear Models for Microarray Data (limma) package () using linear model fitting for statistical testing with empirical Bayes variance smoothing procedure was applied to detection of differentially expressed genes. Obtained P-values were corrected for multiple testing using Benjamini–Hochberg false discovery rate (FDR) procedure (). To identify the biological processes targeted by the 1α,25(OH)2D3-treatment, we used GeneTrail () to analyze the enrichment of up and downregulated VDR target genes into GO categories using default settings., After ligand or no treatment of THP-1 cells, nuclear proteins were cross-linked to DNA by adding formaldehyde directly to the medium to a final concentration of 1% and incubating at room temperature for 15 min on a rocking platform. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating at room temperature for 5 min on a rocking platform. The cells were collected by centrifugation and washed twice with ice cold PBS (140 mM NaCl, 2.7 mM KCl, 1.5 mM KH2PO4, 8.1 mM Na2HPO4·2H2O). The cell pellets were resuspended in 1 ml of lysis buf […]

Pipeline specifications

Software tools lumi, limma, GeneTrail
Databases GEO