Expert view: The development of single‑cell genomics with Smart‑seq

Takara Bio has played a major role in the development of single-cell genomics with the launch of kits such as the automation-ready Smart-seq HT, with a simplified 4-steps protocol. In addition, to meetthe demand for using RNA-seq for degraded clinical samples, we have expanded our offering with a complete sequencing library production kit using low quality and ultra-low quantity RNA: Smart-seq Stranded.

Likewise, the ultra‑sensitive genomic library preparation kits, such as the SMARTer ThruPLEX Plasma‑seq, make it possible to access the circulating DNA sequences present in very small quantities in the blood. This technology is already used for the characterisation of foetal DNA in prenatal diagnosis (NIPT), or tumour DNA in the context of patient follow-up. Furthermore, the techniques for amplification of the complete genome (whole genome amplification – WGA), like that used by the SMARTer PicoPLEX DNA‑seq kit, allows the search for chromosomal abnormalities of oocyte cells in preimplantation diagnosis.

The development of single‑cell genomics has been accompanied by the adaptation of microfluidic reaction in droplets, or in nano‑wells dispensing technologies to process tens to thousands of cells at a time. Takara Bio has chosen the technique of nano‑well dispensing with the SMARTer ICELL8, allowing visualisation of the number of cells in the wells and their selection for processing; development of protocols requiring several dispensing steps; and use with any cell type from the smallest cells or nuclei to the largest (eg, cardiomyocyte or spheroid). ICELL8 already automates, on several hundreds of cells dispensed in the 5184 wells of SmartChip, protocols for the 3’ Differential Expression, Full-length RNA-seq (Smart-seq), Accessible Chromatin analysis (ATAC-seq) or immune profiling receptor (TCR-seq). We have also considered the development of other techniques such as genome sequencing, as well as a combination of techniques (eg, G & T seq) or Pheno-seq.

The future of genomics on single cells unquestionably lies in the combination of approaches currently available, but also the inclusion of proteomics with the use of antibodies. There is no doubt that the SMARTer ICELL8 will play a major role in these combined approaches.