Role of Idax and Rinf in ESC differentiation

In this study we assessed transcriptomic changes that occur due to loss of Rinf or Idax or both during differentiation of ESCs to EBs by subjecting EBs derived from Idax knockout, Rinf knockout or Idax/Rinf double knockout (DKO) ESCs by RNA-seq to identify differentially expressed genes. We studied the role of Idax and Rinf in regulating differentiation gene expression programs by performing RNA-seq of wildtype, Idax knockout, Rinf knockout and Idax/Rinf double knockout embryoid bodies (EBs). EBs were collected at day 6 and total RNA was extracted by (OMEGA E.Z.N.A. Total RNA kit). RNA was quantified by NanoDrop 2000 and 1 µg of RNA was sent to Novogene for mRNA-sequencing analysis (en.novogene.com). Sequencing libraries were prepared by Novogene using NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were subjected to 150-bp paired-end sequencing on Illumina Novoseq 6000 platform. Details for downstream analysis of mRNA-seq data are described in the manuscript methods section.