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RNA-sequencing to identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus

ABSTRACT: RNA-sequencing to identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus

PROVIDER: PRJNA720916 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14197600_1.fastq.gz	Fastqsanger.gz
	SRR14197600_2.fastq.gz	Fastqsanger.gz
	SRR14197595_1.fastq.gz	Fastqsanger.gz
	SRR14197595_2.fastq.gz	Fastqsanger.gz
	SRR14197596_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing to identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus

Project description:To identify differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus, we perfromed RNA-seq. Total RNA from DG deficient in YTHDF2 and the negative control DG were collected and subjected to construct sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB). After sequencencing, the filtered reads were mapped to the mouse reference genome (GRCm38) using HISAT2 v2.0.5 with default parameters. The resulting bam files were fed to featureCounts v1.5.0-p3 to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (cKO vs NC) (three biological replicates per group) was performed using the DESeq2 package (version 1.20.0). Altogether 779 mRNA were differentially regulated, among which 536 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockout of YTHDF2 in granule cells of mouse hippocampus dentate gyrus.

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