Transcriptome profiles of Snap29 knockout and wild-type mouse embryonic stem cells by RNA-seq analysis

Embryonic stem cells have the characteristics of self-renewal and pluripotent differentiation, and have broad application prospects in clinical practice. With the deepening of the research process, ESCs are expected to become the source of donor cells for regenerative medicine and cellular agriculture. Autophagy is a highly conserved catabolic process mediated by lysosomes in eukaryotic cells to meet cellular demands for metabolites and energy. Autophagy is a key process in maintaining cellular homeostasis by removing misfolded or aggregation-prone proteins and damaged organelles. Previous studies have reported that ATG3, ULK1, and other key factors in the formation stage of autophagosomes play a crucial role in maintaining the pluripotency of mouse embryonic stem cells. However, there are few reports on the regulation and molecular mechanism of SNARE proteins that mediate autophagosome-lysosome fusion, including Vamp8, Stx17, and Snap29, on the pluripotency of mESCs. The role of the SNARE protein Snap29 in regulating the self-renewal and pluripotent differentiation ability of mESC remains elusive. To better understand transcriptional landscape and signal transductions, we performed RNA-seq analysis of Snap29 knockout (KO) and wild-type (WT) mESCs at undifferentiated state and mESCs-derived-cells of differentiation . Overall design: We sought to construct a mESCs cell line depleting of the autophagy-specific SNARE gene Snap29 by CRISPR/Cas9 technology. The molecular mechanism was explored through transcriptome analysis to better reveal the conditions of pluripotency maintenance. mESCs with biological triplicates were collected for RNA extraction and RNA-seq analysis simultaneously. We collected Snap29 knockout, wild-type mESCs at undifferentiated state (D0) and differentiated cells at day14 (D14) for RNA-seq analysis.