Integrating the analysis of the cistrome of a transcription factor by ChIP-Seq with the study of its transcriptional output by microarray or RNA-Seq analysis is a powerful approach to elucidate the genomic functions of a tran- scriptionfactor. Recently,weemployedthis approachtodeterminethemechanismofaction by whichthenucle- ar receptor PPAR γ elicits its antitumorigenic effects in lung cancer cells upon activation by TZDs (1). Here we describe in detail the design, contents and quality controls for the gene expression and cistrome analyses associ- ated with our study published in Cell Metabolism in 2014