H > ¼ºñ½º > Next-Generation Sequencing (NGS) > Small RNA
Small RNA
Small RNA sequencing ?
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- Small RNA expression analysis
- Small RNA differential expression analysis
- novel small RNA discovery
- Application to biomarkers and drug targets
½ÇÇè Workflow
Bioinformatics ºÐ¼® Workflow
Small RNA sequencing - ½ÇÇè ÁøÇà °úÁ¤
Sample requirements
concentration | Concentration (ng/§¡) | Quality | |
---|---|---|---|
Total RNA | > 10§¶ (human, mouse, rat) |
> 80 | OD(260/230) > 2.0, OD(260/280)>1.8 is highly recommended |
Small RNA | > 1§¶ (mirVana miRNA isolation kit)> | > 20 |
Sequencing Strategy
50 SE sequencing |
Bioinformatic analysis - contents
contents | |
---|---|
1Â÷ ºÐ¼® | 1. Remove adaptors, low quality tags as well as contaminants to get clean reads 2. Summarize the length distribution of small RNA 3. Analyze common and specific sequences between two samples 4. Explore small RNA distribution across selected genome 5. Identify rRNAs, tRNAs, snRNAs, etc. by aligning to Rfam and Genbank databases 6. Identify repeat associated small RNAs 7. Identify degradated fragments of mRNAs 8. Identify known miRNAs by aligning to designated part of miRBase 9. Annotate small RNAs into several categories based on priority 10. Predict novel miRNAs and their secondary structures by Mireap from unannotated small RNAs 11. Analyze the expression pattern of known miRNAs 12. Family analysis of known miRNAs |
2Â÷ ºÐ¼® | 13. Differential expression analysis of miRNA and cluster analysis (three or more samples should be provided) 14. Target genes prediction of miRNA(the sequence of coding genes should be provided) 15. Target genes GO annotation and KEGG pathway analysis of miRNA 16. Base editing analysis of miRNA(known miRNA) |
3Â÷ ºÐ¼® | º°µµ ³íÀÇ |