RNA-seq analysis of the transcriptome changes on Cenpj depletion cortices at E15.5

Here, we performed RNA-seq to analyze the transcriptome changes on Cenpj depletion cortices at E15.5.RNA-Seq correlation test shows the similarity of the expression patterns between Cenpj+/+ and CenpjCKO was high.By comparing gene expression levels in Cenpj+/+ and CenpjCKO samples, GO term analysis of down-regulated genes in E15.5 CenpjCKO samples showed a significant enrichment of terms related to cell cycle, cell migration, neurogenesis, neuron differentiation and axongenesis, while the up-regulated genes were enriched in cell death, cilium assembly.KEGG signaling pathway analysis revealed that the differentially expressed genes are predicted to be involved in Wnt, MAPK, Hippo, AMPK, Notch, etc. signaling pathways. With Cenpj depletion, we identify a number of genes involved in cilium disassembly were downregulated in developing mouse cortex at E15.5 by RT-PCR, including Kif2a, Kif24, Plk1, Nek2, Ccp110 and Pla2g3, while some cilium assembly genes were upregulated, such as, Rab8a, Mks1, etc., which is in consistent with RNA-seq data, suggesting that RNA-seq data are reliable. The transcriptome changes on Cenpj depletion cortices.本研究通过RNA测序（RNA-seq）分析了胚胎期15.5天（E15.5）Cenpj条件性敲除小鼠大脑皮层的转录组变化。RNA测序相关性分析显示，Cenpj野生型（Cenpj+/+）与Cenpj条件性敲除（CenpjCKO）样本的基因表达模式相似度极高。通过比较两组样本的基因表达水平，对E15.5天CenpjCKO样本中的下调基因进行基因本体（Gene Ontology, GO）富集分析，结果显示其显著富集于细胞周期、细胞迁移、神经发生、神经元分化及轴突发生相关条目；而上调基因则富集于细胞死亡、纤毛组装相关条目。京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes, KEGG）信号通路分析表明，差异表达基因预测参与Wnt、丝裂原活化蛋白激酶（MAPK）、Hippo、AMPK、Notch等信号通路。本研究通过逆转录聚合酶链反应（RT-PCR）验证发现，在E15.5天发育中的小鼠皮层内，参与纤毛解聚的诸多基因在Cenpj敲除后呈下调趋势，包括Kif2a、Kif24、Plk1、Nek2、Ccp110及Pla2g3；而部分纤毛组装相关基因则呈上调趋势，如Rab8a、Mks1等，该结果与RNA-seq数据一致，证实了RNA-seq数据的可靠性。本研究阐明了Cenpj敲除小鼠大脑皮层的转录组变化特征。