Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

Purpose: To identify the role of glycosylation of dentin matrix protein1 (DMP1), S89G-DMP1 point mutation mouse model was created with changing S89 to glycine(S89G). RNA sequencing were performed to compare the transcriptome differences between the neural stem cells or astrocytes separated form S89G-DMP1 and WT mice. Methods: mRNA profiles of astrocytes and neural stem cell separated from S89G-DMP1 and WT were generated by RNA sequencing. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat2(for astrocytes) or with HISAT2o (for neural stem cells). Results: Differential expression analyses with DESeq2 use raw read counts: 762 transcripts were downregulated and 991 transcripts were up-regulated in S89G-DMP1 astrocytes; 475 transcripts were downregulated and 343 transcripts were up-regulated in S89G-DMP1 neural stem cells. All the differential expressed genes were used for Heatmap analysis and KEGG or GO enrichment analyses. Conclusions: Our study represents the detailed transcriptome changes of astrocytes and neural stem cells with deglycosylated DMP1. Overall design: mRNA profiles of astrocytes and neural stem cells separated from adult (10-week-old) S89G-DMP1 or WT mice were generated by RNA sequencing using Illumina.