GSE138512
Next Generation Sequencing Facilitates Quantitative Analysis of LAP2a deficient cells and control cells
Purpose: The goals of this study are to compare the mRNA profiles of LAP2a deficient human adipose-derived stem cells (hASCs) with that of control hASCs by NGS-derived RNA-seq to screen differentially expressed genes and possible involved pathways. Methods: Total RNA was isolated from hASCs transfected with shLAP2a and shNC. RNA sequencing of control and LAP2a deficient cells (each with 2 biological replicates) was performed using BGISEQ-500 sequencing system. Differentially expressed genes (DEGs) between control and LAP2a deficient cells were screened using NOISeq method. KEGG pathway enrichment analysis and Gene Ontology analysis of DEGs were subsequently conducted. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the cell genome. The scatterplot showed that depletion of LAP2a resulted in the upregulation of 106 genes and downregulation of 91 genes. KEGG pathway analysis suggested that LAP2a knockdown led to the change of several important pathways, including cell cycle, MAPK, and NF-?B signaling pathways that are critically related to cell growth and differentiation. Conclusions: Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. Overall design: mRNA profiles of LAP2a deficient human adipose-derived stem cells and control cells were generated by deep sequencing,  in duplicate, using BGISEQ-500.