GSE174522
Next Generation Sequencing Facilitates Quantitative Analysis of primary cultured astrocytes Transcriptomes from neonatal wild type and Spp1 KO retina and optic nerve.
Purpose: The goals of this study are to investigate differential genes expression with RNA-seq between wild type and Spp1 KO retinal and optic nerve astrocytes and then to identify the effected genes after Spp1 knockout Methods: Total RNA was extracted from cultured astrocytes isolated from either C57BL/6 wild-type or Spp1 KO neonatal mice using 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 40 million raw reads per sample were obtained. We mapped sequence reads per sample to the mouse reference genome (GRCm38) and identified 35825 transcripts in astrocytes of wild type and Spp1-/- mice. A total of 3624 differentially expressed genes (DEGs) were identified between wild type and Spp1-/- astrocytes, with a fold change =1.5 and p value <0.05. Among DEGs, 1991 were upregulated and 1633 were downregulated in the Spp1-/- astrocytes. Hierarchical clustering heat map, pathway enrichment and analysis of DEGs were performed. Conclusions: Our RNA-seq dataset represents the differentially expressed genes in theSpp1 KO astrocytes. Overall design: Astrocyes mRNA profiles of wild type  and Spp1 KO neonatal  mice