Single cell seqencing service

BEA core facility is introducing service with the 10X Genomics Chromium platforms allowing solutions for single cell genomics, characterization and gene expression profiling. The Chromium controller device, which is used for separating cells and reagent oligos, has been jointly bought by several departments and groups at KI south campus and is placed at ANA Futura.Questions concerning the single cell service at BEA can be answered by Fredrik Fagerstrom-Billai.

10X Genomics single cell gene expression

The 10X Genomics Chromium single cell system enables the analysis of large cell numbers at the highest capture efficiency. The technology allows for high-throughput single cell transcriptomics of many different cell types. The workflow allows separation and encapsulation of hundreds to thousands of cells per library together with reagent beads into nano-droplets. The single-cell encapsulating process is fast and up to 8 cell populations can be separated in parallel within minutes. After library preparation and sequencing data can be analyzed with the free Cell Ranger and Loupe cell browser software.

Takara SMART seq

For ultra low input amounts and single cell scale transcriptomics we provide different solutions for library preparation. At BEA we have used the SMART-Seq cDNA syntheis reagents from Takara with good results. Input material can be of different origin. Purified Total RNA, cells in lysis buffer or degraded FFPE samples can serve as input material in the analysis.


Smart-seq3, combines full-length transcriptome coverage with a 5' unique molecular identifier (UMI) which enables reconstruction of thousands of RNA molecules per cell. Smart-seq3 enables large-scale characterization of cell types and states across tissues and organisms. Smart-seq3 can be performed from single cells collected in plates or as minibulk with pico amounts of purified Total RNA. BEA collaborates with the single cell core facility in Huddinge to provide this service.