Transcriptome profiles of mouse embryonic stem cells cultured in different conditions by RNA-seq analysis

Pluripotent mouse embryonic stem cells (ESCs) were originally derived and stably maintained on feeder cells such as inactivated mouse embryo fibroblasts, and can generate complete ESC-pups by tetraploid embryo complementation (TEC), the most stringent functional test of naive pluripotency. Remarkably, 2i (inhibitors of Mek and Gsk3β signaling) medium with LIF in the absence of serum and feeders was developed to achieve ground state of mouse ESCs, and also has been successfully used for derivation of germline competent ESCs in other species such as rat. Notably, 2i-culture gives rise to transcriptional profiles and epigenetic landscapes quite distinct from serum-based ESCs. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of ESCs cultured in four different conditions: serum without feeder, serum with feeder, serum with feeder and 2i, and N2B27+2i. We sought to investigate the differentiated expressed genes of N33 ESCs cultured in four conditions: serum without feeder (on gelatin, N33_G), serum with feeder (N33_F), serum with feeder and 2i (N33_F2i), and N2B27+2i (N33_NB2i). ESCs with biological duplicates were collected for RNA extraction and RNA-seq analysis simultaneously.