GSE174523
Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes treated with SB431542, Ro5-3335 and HLM006474 inhibitors.
Purpose: The goals of this study are to investigate differential genes expression with RNA-seq in primary cultured astrocytes treated with the Tgf-beta1 receptor inhibitor SB431542, the Runx1 inhibitor Ro5-3335 and the E2f1 inhibitor HLM006474. Methods: Primary cultured astrocytes were isolated from either C57BL/6 wild-type neonatal mice. Total RNA was extracted from SB431542, Ro5-3335 and HLM006474-treated astrocytes with the RNeasy Plus Micro Kit (Qiagen; 74034). mRNA profiles were generated by deep sequencing using Illumina  NovaSeq 6000. The sequence reads that passed quality filters were aligned to the mouse reference genome (GRCm38) using the STAR software package. Differential expression analysis were performed using the R package DESeq2. qPCR validation was performed using SYBR Green assays. Results: After quality control and data filtering, about 50 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts vehicle, SB431542, Ro5-3335 and HLM006474 group. Differentially expressed genes (DEGs) were analyzed with a fold change =1.5 and p value <0.05. A total of 748 DEGs were identified in SB431542 group with 347 upregulated genes and 401 downregulated genes. A total of 397 DEGs were identified in Ro5-3335 group with 82 upregulated genes and 315 downregulated genes. A total of 856 DEGs were identified in HLM006474 group with 216 upregulated genes and 640 downregulated genes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in the C57BL/6 astrocytes treated with SB431542, Ro5-3335 and HLM006474-treated astrocytes. Overall design: Astrocyes mRNA profiles after treatment with SB431542, Ro5-3335 and HLM006474 inhibitors.