Pluto Bioinformatics

GSE147529: Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice.

Bulk RNA sequencing

Purpose: RNA sequencing (RNA-Seq) analyses of articular cartilage obtained after DMM surgery in Oscar-/- and WT mice. The purpose of this experiment was to demonstrate how the deficiency of Oscar gene affects downstream signal transduction in articular cartilage.; Methods: Articular cartilage mRNA profiles of 10-weeks-old wild-type (WT) and Oscar knockout (Oscar/) mice were performed for the destabilization of the medial meniscus (DMM) and each cartilage tissue sample was harvested from two time-points (2- and 4-weeks after surgery). Sequencing libraries were prepared according to the manufacturers instructions (TruSeq Stranded mRNA Library Prep Kit; Illumina, San Diego, CA, USA). Paired-end sequencing of 101-mer read length was performed using a HISEQ 2500 sequencing system (Illumina). The sequencing quality of raw FASTQ files was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and adapter sequences in reads were eliminated using BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools/).; Results: Usinig RNA-Seq data in articular cartilage tissues from WT and Oscar/ mice subjected to sham or DMM surgery and each cartilage sample obtained from 2- and 4-week time points after surgery, respectively. And we found that significantly enriched pathways in the 1270 common genes.; Conclusions: Our study represents the Oscar gene deficiency analysis of articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. SOURCE: Haeseung Lee (shumians@gmail.com) - Ewha Womans University