Abstract

Massive Analyses of the Transcriptomes of Single Cells

Joakim Lundeberg, Professor, KTH Royal Institute of Technology

Current analysis methods depend on an average transcriptomic footprint of a cell population. Single cells should be analyzed in order to obtain a true cellular profile to analyze cell-to-cell diversity. We approach this question by analyzing spatially resolved gene expression information in single cells at a high resolution taking advantage of high-density barcoded microarrays. mRNA is captured onto the array using poly-A selection but without any RNA extraction steps being performed. This enables short cDNA fragments to be generated using a reverse transcriptase while still being spatially located underneath the cell´s surface. Therefore, isolated cDNA can give a spatially resolved footprint that is highly comparable to the cell it was captured from. The final step is preparing the material for sequencing which facilitates downstream differential expression analysis. This spatial transcriptomics method has been performed on human cancer and fibroblast cell lines and tissues but is widely applicable for varying samples and species of interest including circulating tumor cells. Here we demonstrate the use of spatial transcriptomics technology and the developed STviewer that integrates both histochemical information and gene expression information in single cells.