User:Hoffmeier/Transcriptomics
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)
- Gene expression analysis goes digital. PMID 17687366
- Paired-End Tag (PET), Paired-End diTagging (PET)
- 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
- 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)
- 454, Roche:
- Sequencing by synthesis:
- Solexa, Illumina:
- 1st Generation: GA
- 2nd Generation: GA II (60 000 000 reads, 35 bases)
- Solexa, Illumina:
- 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
- SOLiD (Sequencing by Oligo Ligation/Detection), ABI:
- Pyrosequencing