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RNA-sequencing to idendify differentially expressed mRNAs after knockdown of YTHDF2 in cerebellar granule cells

ABSTRACT: RNA-sequencing to idendify differentially expressed mRNAs after knockdown of YTHDF2 in cerebellar granule cells

PROVIDER: PRJNA643701 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12134638_1.fastq.gz	Fastqsanger.gz
	SRR12134638_2.fastq.gz	Fastqsanger.gz
	SRR12134639_1.fastq.gz	Fastqsanger.gz
	SRR12134639_2.fastq.gz	Fastqsanger.gz
	SRR12134640_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing to idendify differentially expressed mRNAs after knockdown of YTHDF2 in cerebellar granule cells

Project description:To identify differentially expressed mRNAs after knockdown of YTHDF2 in granule cells, we perfomed RNA-seq. Cultured granule cells were infected with lentiviral shYthdf2 or shCtrl. Total RNA was 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 STAR v2.5 with default parameters. The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads, which was further normalized to calculate FPKM. Differential expression analysis of two groups (shYthdf2 vs shCtrl) (three biological replicates per group) was performed using the DESeq R package (version 1.18.0). Altogether 923 mRNA were differentially regulated, among which 587 mRNA were upregulated after YTHDF2 KD. This study provides a gene list which shows differentially expressed mRNAs after knockdown of YTHDF2 in granule cells.

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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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Project description:We performed gene-expression analysis of mouse cerebellar granule cell layer as compared to that of Purkinje cells. DNA microarray analysis detected genes in cerebellar granule cell layer, most of which are classified into functional molecule categories. Our comparative analysis between Purkinje cells and the granule cell layer showed that the characteristic expression pattern in Purkinje cells was particularly represented by M-bM-^@M-^\the neural communication systemM-bM-^@M-^] components. Pukinje cells and granule cell layer of the mouse cerebellum were collected by laser microdissection for RNA extraction and hybridization on Affymetrix microarrays.

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