Single cell microfluidics service lab


We are one of the 3 nodes of HiLIFE Single cell omics platform at University of Helsinki, and offer the following single cell and bulk RNAseq services jointly with Illumina sequencing service at Functional Genomics Unit (FuGU). Most of our libraries are sequenced with the NextSeq500 High output 75 cycle kit producing typically 400 million reads.

NEWS: Single cell Western blot device MILO (ProteinSimple) has just arrived and will be up and running by the end of the summer. Soft lithography station for PDMS chip prototyping and small scale fabrication is also coming during fall 2018.

Drop-seq single cell RNAseq. This cost efficient droplet microfluidics method with barcoded microbeads was originally developed at McCarroll lab at Harvard Medical School (Macosko et al, Cell 2015), and we run the Drop-seq protocol with Dolomite-Bio microfluidics device. Approximately 5% of the input cells will get barcoded, so this method is suitable if your starting material is at least 100 000 cells. The read sequences locate to 3' end of the poly-A mRNA transcripts. If availability of fresh cells is a challenge, we have tested Drop-seq for methanol, DSP and RNAlater fixed cells - please contact for details. We have also set up the Seq-Well protocol for cell capture with microwell slides instead droplets, developed by Shalek lab at MIT (Gierahn et al, Nat Methods 2017). For samples with low number of cells available the Seq-Well is beneficial due to higher cell capture rate than Drop-seq. It needs just 10.000 cells or even less as input.

FACS sorted single cell RNAseq. If your cells of interest are very rare and of limited number, you can also manually pick or FACS sort the desired cell fractions cell by cell into 96-well plates with lysis buffer and well-specific poly-A capture oligos. Our in-house modified protocol with Drop-seq like oligos allow pooled tagmentation, sequencing and analysis pipeline similar to Drop-seq. In addition to current 3' tagging protocol we will soon set this up also to 5' tagging as well as full length coverage versions. Please plan this well beforehand with us and e.g. Biomedicum FACS core.

Bulk RNAseq with Drop-seq chemistry. The FACS sorted single cell method on 96-well plates can be used also as a very cost-efficient bulk RNAseq method for your total RNA samples. Cell fractions of very limited cell numbers can be also lysed and analyzed directly without separate RNA extraction.

Custom microfluidics. In addition to single cell droplet capturing, the Dolomite-Bio microfluidics device with 3 pressure chambers/flow controllers and high speed camera microscope can be adapted to various other assays using chip designs available at Dolomite-Microfluidics web catalogue. Set-up costs of new assays will be additionally charged. We can also help in design and production of custom PDMS microfluidic chips at Micronova Nanofabrication Centre of Aalto University and VTT in Espoo, and during the fall all the basic lithography devices will be set up to Meilahti as well.

DNA, RNA and library quality checks. We use Perkin Elmer LabChip GX Touch HT capillary electrophoresis system to check the DNA or RNA integrity and NGS library size and concentration of up to 384 samples per each run. Especially for large numbers of samples LabChip is very cost efficient and quick.

Bioinformatics of single cell/bulk RNAseq data. If you are not familiar with RNAseq data analysis, we can teach you how to process the Illumina raw FASTQ files into genome aligned digital expression matrix, and further into biologically meaningfull cell type cluster and differential expression data. If you are not comfortable with R and command line working, we can guide you how to analyze your own data with user friendly CSC Chipster platform in which the e.g. Drop-seq pipeline and Seurat tools have been installed and more single cell tools to be added in future.