Work Log - 02/22

Transcript

1. Work Log 2/22 Liang Bo Wang Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine
2. Systematic bias of small RNA quantization using NGS small RNA sequencing Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 2 Digital Gene Expression profile = DGE profile
3. Protocols for sample preparation  Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 3
4. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 4 •  Fig a: different protocol affects expression rate •  Fig b: Systematic bias -> bias is reproducible
5. Expression changes drastically with single base alteration •  Great for detecting isomiRs •  The adapter sequence affects miRNA expression Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 5
6. Conclusion & Notes Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 6 •  Bias is possibly due to preference of RNA ligase •  Currently, all my datasets use SREK-like protocol •  Illumina’s Small RNA Sample Prep Kit •  Careful not to mix datasets of different protocols •  Later papers show some ways to eliminate or correct the bias •  no consensus reached yet •  Differential expression is recommended •  For precise quantization, still use qRT-PCR •  quantitative Reverse Transcription PCR
7. Bioinformatics and Biostatistics Core, NTU Center of Genomic Medicine 7 2011