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| Status |
Public on Mar 26, 2020 |
| Title |
Global gene expression of Oscar Knock-out (KO) mice with Wild Type (WT) mice. |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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 manufacturer’s 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.
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| Overall design |
Articular cartilage mRNA profiles of 10-weeks old wild type (WT) and Oscar-/- mice were generated by RNA sequencing (each group, n=10) using Illumina hiseq2500.
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| Contributor(s) |
Lee Sy |
| Citation(s) |
32859940 |
| |
| Submission date |
Mar 25, 2020 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Haeseung Lee |
| E-mail(s) |
haeseung@pusan.ac.kr
|
| Organization name |
Pusan National University
|
| Department |
College of Pharmacy
|
| Street address |
63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu
|
| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA615179 |
| SRA |
SRP254026 |
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