Microarray analyses, RNA amplification, labeling, hybridization and detection were performed following the protocols supplied by Applied Biosystems using the
corresponding kits (Applied Biosystems). The microarray data were extracted using the Bioconductor limma package [39] (
link) and median normalized. Data quality was determined using a QC procedure [40] (
link). Data were normalized using NeONORM with
k = 0.02 [41–43] . Subtraction profiling was performed as described previously [44,45] using the CDS test [46] (
link). Differentially expressed genes were classified using Ingenuity Pathway Analysis software to detect network- and pathway-enrichments. Transcriptome data were deposited in the public database MACE (
http://mace.ihes.fr) using Accession Nos: 3167467256 (5-aza-dC treatment HEK293 cells), 2426124024 (RA treatment HEK293 cells), 2147989240 (CBP overexpression HEK293 cells), 2267526904 (RA treatment of TDG(TDGP65A)/CBP expressing HEK293 cells), 2586598264 (5-aza-dC treatment COS-7 cells), 2283559800 (RA treatment COS-7 cells), 2740738936 (CBP overexpression COS-7 cells), 2763807608 (RA treatment of TDG/CBP expressing HEK293 cells), 2549898104 (RA treatment of TDGP65A/CBP expressing HEK293 cells), 2901761912 (wild-type TDG overexpression in HEK293 cells) and 2890751864 (TDG P65A overexpression in HEK293 cells).
Léger H., Smet-Nocca C., Attmane-Elakeb A., Morley-Fletcher S., Benecke A.G, & Eilebrecht S. (2014). A TDG/CBP/RARα Ternary Complex Mediates the Retinoic Acid-dependent Expression of DNA Methylation-sensitive Genes. Genomics, Proteomics & Bioinformatics, 12(1), 8-18.