GSE133661
RNA-seq approach to analysis of gene expression profiles between wild-type and C19orf12 knockdown A549 cell line
The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) in human lung cancer cells. The mRNA profiles of wild-type and C19orf12 knockdown A549 cells were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with Burrows–Wheeler Aligner (BWA) and Bowtie2. we sequenced 6 samples of human species using RNA-Seq technology, averagely generating 24,382,600 raw sequencing reads and 24,299,184 clean reads after filtering low quality. We identified 20826 transcripts in the of WT and C19orf12 knockdown A549 samples with BWA workflow. Approximately 2% of the transcripts showed differential expression between the WT and C19orf12 knockdown A549 cells, p value <0.05. Altered expression of 21 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. We conclude that RNA-seq based transcriptome characterization would providing clues for better understanding of gene function. Overall design: mRNA profiles of sh-scramble (wild-type) and C19orf12 knockdown A549 cell line were generated by deep sequencing, in triplicate, using Illumina hiseq4000.