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.


 * Paired-End Tag (PET), Paired-End diTagging (PET)
 * 1) Paired-end diTagging for transcriptome and genome analysis.


 * 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.

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