The genome determines changes of the transcription profile upon environmental changes and finally determines how a cell reacts. A comparative genome and transcriptome analysis of the same sample is a tool to explain changes in the transcriptome by features within genome. In order to avoid a mixed transcription profile from multiple cells, it is necessary to analyze a small cell number. For a detailed analysis of the genome and transcriptome, next-generation sequencing (NGS) is a useful method. However, it requires an amount of nucleic acid much higher than that present in a few cells. Therefore, whole genome amplification (WGA) and whole transcriptome amplification (WTA) is prerequisite for NGS. 

Here, we describe how the genome and the transcriptome can be amplified simultaneously from a few cells in a highly parallel and comparable process. We present application data from cancer and endothelial cells.