Transcriptome analysis using RNA sequencing of the neurospheres from EGFL7-/- versus wildtype mice

We assessed the effect of a deletion of epidermal growth factor like 7 (EGFL7) on neurogenesis. Here, we assessed differential gene expression in neuropheres of EGFL7-/- versus wildtype mice using RNA-sequencing. EGFL7 deficiency increases the rate of proliferation of neural stemm cells (NSC), and increases the velocity of maturation and integration of adult born mature neurons into existing networks. Hence, EGFL7 pushes NSCs towards quiescence and neural progenitors towards differentiation. Differential genes expression was used to assess underlying mechanisms. The experiment was done in two sequential analyses, experiment-1 comprised 6 sample per genotype (single end reads), and experiment-2 had 4 samples per genotype (paired end reads). The final analysis was done with a pooled dataset. A total number of 19709 genes was reliably detected in >8 valid samples out of 20 in total. GSEA gene set enrichment analysis was used for gene ranking and identication of top up- and downregulated genes and evaluation of their functions. VENN diagrams were used to assess the agrement of Exp1 and Exp2 and the combined analysis. Overall design: RNA from neurospheres from the subventricular zone (d3) and the hippocampus (d5) was analyzed by RNA sequencing of 10 biological replicates per genotype (EGFL7 versus wildytpe) using an Illumina Novaseq600 system.