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Gene Expression Profiling

Dynamic Range of Gene Expression Detection Platforms
Microarrays = 2-3 Logs
SOLiD™ System = 5 Logs
TaqMan® Assays = 7-8 Logs

Analysis of global gene expression patterns provides valuable insight into the role of differential expression in normal biological and disease processes.

Microarrays: limited dynamic range and ability to detect novel exons
High density microarrays have been used to globally assay mRNA expression levels, however, microarrays are limited in their dynamic range and can be relatively ineffective at measuring low copy genes. Furthermore, traditional microarray approaches depend upon 3’ biased sample preparation and hypothesis driven probe design, limiting their ability to detect novel exons or differentiate between splice variants.

SOLiD™ SAGE™ System: For quantification of gene expression

The SOLiD™ Serial Analysis of Gene Expression (SAGE™) System provides a highly sensitive, hypothesis-neutral method for quantifying gene expression levels on a genome-wide scale. This method, which determines mRNA expression levels by sequencing unique sequence tags isolated from the 3’ ends of mRNAs, has significant advantages over microarray technologies:
  • Detects known and novel mRNAs.
  • Is highly reproducible, with a dynamic range that is orders of magnitude greater than microarrays.
  • Detects expression of transcripts from < 1 copy per cell to over 100,000 copies per cell, corresponding to a dynamic range of > 105.
The sequencing-based SOLiD™ SAGE™ Kit with Barcoding Adaptor Module and analysis software provides an optimized and streamlined protocol enabling high-throughput analysis and quantification of genome-wide expression levels of both traditional poly(A) and non-poly(A) transcripts. A limited number of steps developed for SAGE™ are used to generate a library of 27-bp “3’ tags” for all the transcripts in a cell, followed by SOLiD™ System sequencing. By isolating 27 bp 3’ tags, highly accurate quantification of expression profiles and simplified mapping are achievable with significantly less reads allowing for more samples per run. The Barcoding Adaptor Module in combination with any of the SOLiD™ RNA Barcoding Kit enables multiplexing and cost effective gene expression profiling across many samples.

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