Transcriptomes of miR-290-295 KO mESCs treated with siPOOLs against the transcription factor Tfap4. Transcriptomes of miR-290-295 KO mESCs treated with siPOOLs against the transcription factor Tfap4

In order to identify direct microRNA targets in mouse embryonic stem cells (mESCs), we knocked out microRNA effector genes, profiled their transcriptomes and integrated the data with additional published OMICs data sets. To validate the analysis, we generated miR-290-295 KO mutant cell lines, assessed the transcriptome profile and compared the observed misregulation to the predictions of the analysis. We identified the transcription factor Tfap4 as novel potential direct and functional target of miR-290-295. To assess the role of Tfap4, we rescued its expression in the miR-290-295 KO cell line using siPOOLs and profiled the transcriptome. Overall design: Transcriptomes of WT mESCs and miR-290-295 KO E14 mESCs with and without siPOOL treatments for Tfap4 and a negative control were generated in biological duplicates using QuantSeq kit. WT and miR-290-295_KO cells were prepared and sequenced together, as were all 4 siPOOL-treated samples.