RNA-sequencing to idendify differentially expressed mRNAs after knockdown of YTHDF2 in cerebellar granule cells
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. Overall design: 3 replicates in each group