基于RNAseq技术的肝细胞肝癌转录组学研究(5)

2.1 RNA extraction.....................................................................................................60

2.2 RT-PCR.................................................................................................................60

2.3 Real time RT-PCR.................................................................................................61

2.3.1 TaqMan RT-PCR................................................................................................61

2.3.2 SYBGreen RT-PCR:...........................................................................................61

2.4 Primers or Probes and PCR conditions for real time RT-PCR..............................61

2.5 Global analysis of RNA-seq data....................................................................65

2.5.1 Alignment of sequenced reads.............................................................................65

2.5.2 Evaluation of data quality and sequencing depth.................................................65

2.5.3 Differential expression analysis of gene, exon and novel exon-exon junction.....65

2.5.4 Comparison between RNA-seq and public microarray data................................65

2.5.5 Functional annotation and positional gene enrichment analysis...........................65

2.5.6 Identification of novel differentially expressed exon-exon junctions...................65

3 Results..........................................................................................................................65

3.1 Differential gene expression and validation..........................................................65

3.2. The chromosome locations of DEGs...................................................................68

3.3 Functional annotation of DEGs.............................................................................69

3.4. Exon expression level analysis............................................................................71

3.5 Identification of novel DE exon-exon junctions...................................................76

4 Discussion....................................................................................................................77

conclusion...............................................................................................................................81

Supplementary........................................................................................................................82

Supplementary 1.............................................................................................................82

Supplementary 2.............................................................................................................82

Supplementary 3.............................................................................................................88

Supplementary 4.............................................................................................................89

Supplementary 5.............................................................................................................89

Supplementary 6.............................................................................................................90

References...............................................................................................................................92

个人简历和研究成果..........................................................................................................107

致 谢..............................................................................................................................108