We curated a set of ES perturbations and differentiation states from publicly available sources. Specifically, we utilized the NCBI e-utils (http://eutils.ncbi.nlm.nih.gov/) to programmatically identify all published datasets containing keywords associated with embryonic stem cells. We filtered the list to only include mouse data sets that were generated across one of three commercial array platforms (Affymetrix, Agilent, and Illumina). Following this approach, we manually curated the list to include datasets associated with ESC perturbations (genetic deletions, RNAi, or chemical perturbations) and differentiation or induced differentiation profiles. This curation yielded 41 GEO datasets corresponding to >150 samples.
