Smart-seq plate-based single cell sequencing

Developed in 2014 by the Sandberg lab at KI, the Smart-seq2 chemistry paved the way for single cell RNA sequencing. By using the SMART technique of template switch, full-length sequencing of the transcriptome became possible on a single cell level, enabling detection of thousands of genes per cell (2500-6000 depending on cell type).

The Smart-seq3 chemistry is an evolution of Smart-seq2, offering increased depth (3500-9000 genes/cell, depending on cell type) while also introducing UMI based gene counting for more accurate gene expression counts. The full-length information is also preserved, and less starting material is required.

SICOF supports both chemistries, but we have noticed problems with robustness and reproducibility with Smart-seq3. In addition, Smart-seq3 chemistry depends on the successful sequencing of very long fragments, which are rarely captured on Illumina sequencing platforms. Thus, we strongly recommend Smart-seq2, especially for Smart-bulk (see below).

Smart-Bulk RNA-seq

We use SMART chemistry to study bulk cells/organisms in a high-throughput manner. Cells or small tissues are lysed and then processed as single cells, but with adjustment for the higher concentration in starting material. This application excels when the starting material is very low/bad quality, or when a lot (100+) of RNA samples need to be sequenced. For standard bulk RNA-seq of fewer samples, we recommend you contact BEA.