User:Hoffmeier/Transcriptomics

Gene expression profiling

Profiling Methods

Tag-based sequencing strategies are efficient for analyzing DNA fragments in transcriptome characterization and genome annotation studies:

• Expressed Sequence Tag
• Serial Analysis of Gene Expression (SAGE) (BsmFI, 10-14 bp tags)
  • LongSAGE (MmeI, 18-20 bp tags)
  • SuperSAGE (EcoP15I, 26-28 bp tags)
• Digital Gene Expression tag profiling (DGE)

1. Gene expression analysis goes digital. PMID 17687366

• Paired-End Tag (PET), Paired-End diTagging (PET)

1. Paired-end diTagging for transcriptome and genome analysis. PMID 18265396

• GIS-PET: Gene Identification Signature (GIS) analysis, which covalently links the 5' and 3' signatures of each full-length transcript into a Paired-End diTag (PET) structure

1. Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. PMID 15782207

Sequencing Methods

• Next-Generation Sequencing (NGS), Massively Parallel Sequencing (MPS), Flow Cell Sequencing
  • Pyrosequencing
    • 454, Roche:
      • 1st Generation: GS 20 (200 000 reads, 100 bases)
      • 2nd Generation: GS FLX (400 000 reads, 200-300 bases)
      • 3rd Generation: GS Titanium (1 000 000 reads, 400-500 bases)
  • Sequencing by synthesis:
    • Solexa, Illumina:
      • 1st Generation: GA
      • 2nd Generation: GA II (60 000 000 reads, 35 bases)
  • Sequencing by ligation:
    • SOLiD (Sequencing by Oligo Ligation/Detection), ABI:
      • 1st Generation: v1.0
      • 2nd Generation: v2.0 (120 000 000 reads, 35 bases)
      • 3rd Generation: v3.0