Fig. 7

Fig. 7 Shoc2 knock-out disrupts gene expression of the sox10-positive cells.

(A) Cartoon illustrating the workflow used to analyze transcriptome of sox10: RFP ⁺ cells. Total RNA was isolated from the FACS-sorted sox10: RFP ⁺ cells, followed by RNA-seq analysis. Data was profiled to identify Enriched GO Biological Processes from Category Compare (Flight et al., 2014). Nodes represent enriched annotation of DEGs. Edges represent relationship between annotation sharing high number of genes with p-value cutoff 0.001 and edge weight greater than 0.90. (B) The top 15 protein classes of 351 differentially expressed genes (FDR≤ 0.05) analyzed with PANTHER pathway analysis. (C) DEGs were selected from the protein class of “Extracellular matrix proteins”. Total RNA was extracted from sox10:dsRed ⁺ cells of control and shoc2 null larvae at 6 dpf and mRNA expression were quantified by qPCR. gapdh is a control mRNA. The results represent an average of three biological replicas. The data are presented as the Log₂fold change of the mRNA levels in the shoc2 null larvae normalized to WT larvae. Error bars indicate means with SEM. ∗p<0.05, ∗∗p<0.01, ∗∗∗p<0.001 (Student’s t-test). (D.) DEGs were selected from the protein class of Extracellular Matrix Proteins. Total RNA extracted from sox10:dsRed ⁺ control and shoc2 null larvae at 6 dpf and levels mRNA expression were quantified by qPCR. The data are presented as the Log₂fold change of the mRNA levels in the shoc2 null larvae normalized to WT larvae. gapdh is a control mRNA. The results represent an average of three biological replicas. Error bars indicate means with SEM. ∗p<0.05, ∗∗p<0.01, ∗∗∗p<0.001 (Student’s t-test). (E) Control and shoc2 null larvae were harvested for immunoblotting at 6 dpf. The expression of indicated proteins was analyzed using specific antibodies by WB. (F.) Total RNA extracted from the dissected trunk of WT and shoc2 null larvae at 6 dpf. mRNA expression of sox9a was quantified by qPCR at 6dpf. The data are presented as the Log₂fold change of the mRNA levels in the shoc2 null larvae normalized to WT larvae. Gapdh is a control mRNA. The results represent an average of three biological replicas. Error bars indicate means with SEM. ∗p<0.05, ∗∗p<0.01 (Student’s t-test). (G) Total RNA extracted from control and shoc2 null larvae. mRNA expression was quantified by qPCR at 5 or 6 dpf. The data are presented as the Log₂fold change of the mRNA levels in the shoc2 null larvae normalized to WT larvae. Gapdh is a control mRNA. The results represent an average of three biological replicas. Error bars indicate means with SEM. ∗p<0.05, ∗∗p<0.01 (Student’s t-test). (H) Ventral view of WT and shoc2 morphant embryos showing expression of sned1 in 3 dpf larvae. Aberrant expression patterns of sned1 are evident in shoc2 morphants. The graph shows the frequency of abnormal patterns. The total number of embryos used in the statistical analysis is indicated. The results represent an average of three biological replicas. Statistically significant differences between shoc2 MO and control MO according to the Pearson’s chi-squared test are indicated by ∗p<0.05, ∗∗p<0.01, ∗∗∗p<0.001. (I) Total RNA was extracted from control and shoc2 null larvae at 6 dpf. The levels of sned1 mRNA expression were quantified by qPCR at 5 and 6 dpf. The data are presented as the Log₂fold change of the mRNA levels in the shoc2 morphant larvae normalized to control larvae. gapdh is a control mRNA. The results represent an average of three biological replicas. Error bars indicate means with SEM. ∗p<0.05, ∗∗p<0.01 (Student’s t-test).