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

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

PROVIDER: PRJNA433679 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6703960_1.fastq.gz	Fastqsanger.gz
	SRR6703960_2.fastq.gz	Fastqsanger.gz
	SRR6703959_1.fastq.gz	Fastqsanger.gz
	SRR6703959_2.fastq.gz	Fastqsanger.gz

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

Project description: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.

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Project description:The goal of the study was to compare gene expression of P0 wild-type, P0 Fezf2-/- cortices, and Fezf2-/-; Fezf2-EnR cortices. Total RNAs were isolated from P0 cortices dissected from wild-type (n=3), Fezf2-/- mice (n=4), and Fezf2-/-; Fezf2-EnR cortices (n=2), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA PolyA library preparation guide.The libaries were pair-end sequenced (150nt per end). Differentially expressed genes were identified by DESEQ.

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