KCNQOT1 ChIRP seq and perturbation epigentic profiles [MeDIP]

To study the molecular function of lncRNA KCNQOT1, we performed ChIRP-seq HEK293T cells, and we knocked it down in NIH3T3 and HEK293T cells, and created knockout of the repeat-rich and non-repeat regions of KCNQOT1 separately in HEK293T cells, then performed H3K9me3 ChIP-seq, DNA methylation MeDIP-seq and RNA-seq in the perturbed and control wild type cells. Overall design: DNA methylation status was analyzed by MeDIP-seq in HEK293T EV, KCNQ1OT1_K KD, WT, K non-rep KO, and K rep KO cells.