Fig. 3

Gene expression profiles in ES cells differentiated with bexarotene or RA. a Mouse ES cells (D3 line) were grown as hanging drops for 2 days and then in suspension for an additional 5 days, to allow the formation of EBs in the presence or absence of bexarotene (Bex, 50 nM) or RA (10 nM). Undifferentiated ES cells were analyzed in parallel (ESCs). Total mRNAs isolated from the cells were subjected to Affymetrix microarray analysis. Primary analysis and quality control was performed using the Affymetrix Expression Console (version 1.1.2637.26569). Probe intensity data was normalized using robust multi-array average (RMA), and a threshold of ±1.5-fold was used to define differential expressed between each condition. Euclidean distance-based clustering was used to visualize the expression of differentially expressed genes. Raw and processed data are deposited in NCBI’s Gene Expression Omnibus (GEO) database, under accession number GSE94779. Standardized values of expression (log₂) for genes that showed a difference in expression greater than ±1.5-fold between bexarotene-treated EBs and untreated EBs (Ctl). b GO terms associated with genes differentially expressed following bexarotene treatment found using the DAVID. c Expression of selected genetic markers for mesoderm specification (T), mesoderm development (Meox1, Pax3, Pax7) and cardiac specification (Isl1, Kdr). Values are given as difference in expression (log₂) between the EBs and ESCs. Inset is the relative mRNA levels of Meox1 validated by qRT-qPCR analysis and plotted as fold change relative to untreated EBs after being normalized to GAPDH. d Expression of early myogenic transcription factors given as the fold change relative to ESCs. Values in ESCs are indicated by a dashed line