GSE192879
To perform a standard RNAseq experiment to evaluate the impact of the knockout of Zeus gene(CG9573) in D. melanogaster
This experiment was designed to study the transcriptional alternations using RNA-seq technique. RNA materials were collected and sequenced with multiple experimental groups in tri-plicates as follows: control-knockout-replicate 1~3 (KO-Ctrl__1~3), Zeus-knockout-replicate 1~3 (KO-Zeus__1~3), for RNA-sequencing. In total, 6 sequencing files were downloaded from the genomic core facility, University of Chicago. The aims of this analysis are to 1) conduct quality control (QC) assessment on the original raw sequencing data, 2) map sequencing reads to target species, 3) identify differentially expressed (DE) protein-coding genes per comparison. Through assessing the quality of original raw sequencing data, good base-wise quality was revealed in average in all samples, indicating a high confidence on the base call. Adapter/primer sequences are absent from reads; therefore, trimming of sequencing reads was skipped prior to downstream RNA-seq analysis. Overall, around 94.89% of reads were successfully mapped to the fruit fly genome model in RNA-seq data. All RNA samples were used for further downstream identification of differentially expressed (DE) mRNA genes in individual pairwise comparison. Several commonly used tools (DESeq2, edgeR, and limma) were utilized for the identification of DE mRNA between pairwise groups. Using the criteria of fold change no less than 1.5 and FDR (False Discovery Rate) less than 0.1). Pairwise comparison, KO-Zeus/KO-Ctrl, were conducted. Overall, we find Zeus regulated the expression of 661 differentially expressed genes (DEGs) based on combination of three tools. Venn diagram was further depicted to present the consensus/overlapped DE gene sets detected across different methods. Overall design: Identification of DEGs between Zeus-KO mutant and WT in testis in Drosophila melanogaster.