Amplification products generated by the TransPlex® WTA and Complete WTA2 kits are suitable for microarray target for expression analyses, and can be incorporated into existing Affymetrix workflows through a procedure known as Pico Profiling1,2. Pico Profiling is comprised of a modified Affymetrix GeneChip® Mapping 10K Assay Protocol3 for fragmentation and labeling of the amplification product, followed by a modified hybridization procedure taken from the Affymetrix GeneChip® Expression Analysis Technical Manual4.
The WTA amplification product is double-stranded cDNA. Fragmentation and labeling is accomplished using the following Affymetrix products.
The Transplex WTA and Complete WTA2 RNA amplification kits are designed to representatively amplify RNA of marginal quality, such as degraded RNA extracted from formalin-fixed paraffin-embedded (FFPE) samples or small quantities of RNA damaged by laser capture. In addition, the kit is equally suitable for high-quality RNA. Pico Profiling3,4 is a complete process for isolation and purification of total RNA from single or very small numbers of cells, followed by Complete WTA2 amplification and analysis on Affymetrix expression microarrays. Moreover, Pico Profiling steps subsequent to RNA isolation and purification can be used for any quantity of input RNA.
When working with small RNA samples, follow the Pico Profiling protocol in its entirety; otherwise, enter the protocol following amplification at the step "cDNA Fragmentation”. Follow procedure presented on the Institute for Research in Biomedicine (IRB, Barcelona) Functional Genomics Core Facility website as outlined.2
Follow procedure presented on the Institute for Research in Biomedicine (IRB, Barcelona) Functional Genomics Core Facility website as described.3
Note the following points: