Sequence-independent Selective Amplification of mRNAs over rRNAs
Poster Nov 29, 2010
John Arrand1, Sim Sihota1, Wenbin Wei1 and Guido Krupp2
Standard mRNA amplifications for "All-Exon" microarrays and for bacterial RNAs are impossible with small samples (< 100 ng total RNA) and with
degraded RNAs, because removal of rRNAs must precede universal, non-selective RNA amplification (Affymetrix and Ambion kits, respectively).
This pre-treatment with magnetic beads is cumbersome, requires high amounts of starting material (>0.5 µg total RNA), is not universal for all species
and degraded RNAs are not suitable. Omission of this step results in lost sensitivity .
However, AmpTec's unique TRinucleotide primer strategy renders reverse transcriptions selective for mRNA (fragments) and it provides sequenceindependent, preferential 3'-proximal priming. This eliminates the rRNA removal step, thus high mRNA amplifications (input of <1 ng total RNA
yields >10 µg amplified RNAs), and the use of degraded RNAs are possible. A first Exon Array study with saliva RNA (<4ng of degraded RNA) is now in press .
 Pepper et al., 2007 “A Core Lab Case Study: Exon Array Challenges and Opportunities” Affymetrix Application Note.
 Hu et al., 2008 (Wong lab at UCLA) “Exon-level expression profiling: a comprehensive transcriptome analysis for oral fluids.”
Clinical Chemistry 54:5 (E-publication ahead of print).
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Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes. The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. This, in turn, is likely to influence the expression of nearby or more remotely located genes to alter beta cell function. At present, however, detailed molecular and functional analyses are still lacking for most of these variants. We recently analysed one of these loci and mapped five causal variants in an islet-specific enhancer cluster within the STARD10 gene locus. Here, we aimed to understand how these causal variants influence b-cell function by alteration of the chromatin structure of enhancer clusterREAD MORE
Early life stress (ELS) is highly associated with development of psychopathology
and mood disorders in adulthood. Genetic studies have identified variation in the gene calcium voltage-gated channel subunit alpha1C (CACNA1C) to increase risk for several psychiatric disorders. This poster assessed the expression of Cacna1c following prepubertal stress.