RNAseq analysis of EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA

We constructed EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA to select differentially expressed genes and transcripts EC109 cells transfected by lncRPL34-AS1 plasmid and scramble pcDNA were used for RNA-seq. RNA quantification and quality assurance were evaluated by NanoDrop ND-1000, and RNA integrity and gDNA contamination tested by standard denaturing agarose gel electrophoresis. After oligo dT enrichment (rRNA removal) of 1~2ug selected total RNA, the sequencing libraries were constructed using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The mixed different sample libraries were sequenced by IlluminaNovaSeq6000 sequencer, raw sequencing data performs sequencing quality control (QC) to evaluate sequencing data analysis. The Solexa pipeline version1.8 (Off-Line Base Caller software, version1.8) software was used for image processing and base recognition. FastQC software evaluates the sequencing quality of unconnected reads (using cutadapt to remove 3 'and 5' connectors). The reference genome was compared by Hisat2 software. The transcriptional abundance was estimated by using StringTie software with reference to the annotated information of the official database. The R software Ballgown was used to calculate the FPKM at gene level and transcript level, and the differences of expression at gene level and transcript level were calculated respectively. Based on the PCA analysis and correlation analysis of gene and transcript expression level, the differentially expressed genes were analyzed by scatter plot, volcano diagram, cluster diagram, GO function and KEGG pathway significant enrichment