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RNA-seq in differentiation of WT129 mESCs to neurons

ABSTRACT: RNA-seq in differentiation of WT129 mESCs to neurons

PROVIDER: PRJEB33696 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3453510.fastq.gz	Fastqsanger.gz
	ERR3453520.fastq.gz	Fastqsanger.gz
	ERR3453511.fastq.gz	Fastqsanger.gz
	ERR3453521.fastq.gz	Fastqsanger.gz
	ERR3453512.fastq.gz	Fastqsanger.gz

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RNA-seq in differentiation of WT129 mESCs to neurons

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Project description:To study the cell composition and gene expression profile in the mesendoderm differentiation of WT and PHD2 knockout, we performed scRNA-seq on the cells collected from the differentiation of WT and PHD2 knockout AB2.2 mESCs at differentiation day 4. PHD2 knockoutout mESCs were constructed by CRISPR/Cas9. The differentiation was performed using a non-lineage tendency differentiation protocol.

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Quantitative Analysis of Wild Type(wt) and Setd2 knockout(ko) mESCs Transcriptomes [RNA-Seq]

Project description:Purpose: This study aimed at exploring the deregulated genes in setd2 knockout mESCs compared with wt, more particularly to find the mechanism controlled by setd2,which was required for endoderm differentiation. Methods: Setd2 wt and ko mESCs were generated by deep sequencing, using Illumina GAIIx. Using Avadis NGS (version:1.3) software to analyze the sequence reads that passed quality filter to acquire the expression level of all genes. qRT–PCR validation was performed usingSYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 80 million sequence reads per sample to the mouse genome (build mm9) and identified 17,827 transcripts in the sted2 wt and ko mESCs. About 2,516 genes were deregulated in setd2 ko mESCs, more than 10 genes were validated using qRT-PCR. Conclusions: Through RNA-seq,we noticed that a subset of genes that related to MAPK signaling pathways were down-regulated in ko mESCs. This provided a bridge to connect setd2 and mESCs endoderm differentiation. One wt and one ko mESCs were generated by deep sequencing, using Illumina GAIIx.

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