The single-cell tagged reverse transcription (STRT) method with unique molecular identifiers (UMIs) is a quantitative single cell sequencing method developed by Sten Linnarsson’s laboratory (e.g. Islam 2014). Recent development of the method by introduction of a second index and a custom made WaferGen 9600 micro well chip (Hochgerner 2017) has scaled up the method from the previously offered Fluidigm C1 96-well chip. In this STRT-seq-2i method the samples can either be dispensed from a single cell suspension by limiting dilution or dispensed by FACS into the wells. When using limiting dilution each well is imaged and automated cell selection is used to select up to 3000 cells per chip. The limit of 3000 cells per chip is due to the current set of 32 unique index primers selected with the Poisson distribution limit in mind. Cell loading is done at eight positions and thus 1-8 samples can be loaded in each chip by limiting dilution. So far, FACS dispension has been set up in collaboration with the SciLifeLab National Mass Cytometry Facility and currently up to 2400 wells can be dispensed per chip. In the library preparation each sample is tagged with a unique combination of indexes and then all samples are pooled before sequencing. We do 50 basepair single-read sequencing and deliver annotated gene expression data. We don’t offer any project specific downstream data analysis.

 Limiting dilutionFACS
No of cellsUp to 3072 (~2000)Up to 2400
No samples1-8No limit
Sample typeCells, nucleiCells, nuclei