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 . Most of our libraries are sequenced with the NextSeq500 High output 75 cycle kit producing up to 400 million reads, or with the new NovaSeq platform at .
Single cell RNAseq
The cost efficient DropSeq droplet microfluidics method with barcoded microbeads was originally developed at at Harvard Medical School (), and we run the protocol with . 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. We have also set up the Seq-Well protocol for cell capture with microwell slides instead droplets, developed by at MIT (). 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.
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.
Single cell Western blotting
We have the device for expression level and size isoform detection of any protein from up to 1000 single cells per slide. Our Agilent scanner reads red and green fluorescence, and several stripping rounds can be performed for the slides for detection of multiple proteins from the same cells.
Automated capillary Western blotting
With this system you can run and stain up to 24 samples in each 3h run, with very small sample and antibody volumes, and minimal hands on time. JESS reads chemiluminescent, fluorescent (IR and NIR) and total protein signals, all even from the same capillary.
Custom microfluidic chip fabrication
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 . Set-up costs of new assays will be additionally charged. We can also help in design and production of custom PDMS microfluidic chips at of Aalto University and VTT in Espoo. We have also our own local cleanroom with and aim to organize annually a course for PhD students.
Chip and slide imaging
We have the by Meros, and .
DNA, RNA and library quality checks
We use Perkin Elmer 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 platform in which the e.g. and tools have been installed and more single cell tools to be added in future.