Services

    We provide services for single-cell and spatially resolved gene expression and protein profiling as a part of the national Biocenter Finland infrastructure network.

    Recent methodological advances have enabled highly multiplexed measurements of various modalities at single-cell level. Such analyses can provide important insights on the composition of complex tissues, reveal developmental trajectories, and even lead to the discovery of entirely new cell types. We support high-level research by providing access to methods that allow such unbiased characterisation of cellular identities and phenotypes from diverse types of samples.

    As a part of the national Biocenter Finland single-cell omics technology platform service, our mission is to provide a one-stop solution for single-cell analyses. This is achieved by seamless integration with the services provided by other core facilities, including the Cell Imaging and Cytometry Core, the Finnish Functional Genomics Centre and the Medical Bioinformatics Centre, bringing together all the expertise and infrastructure that is needed for carrying out cutting edge research projects. At the moment our services consist of high throughput single-cell transcriptomics (RNA-sequencing) and single-cell protein profiling (mass cytometry). In addition, we provide scientific consultation and engage in research collaborations focused on development and implementation of new methods and technologies.

    Read online or download our brochure (PDF)

    Single Cell Applications

    Single-cell Sequencing

    Transcriptomics (scRNA-seq)

    Overview
    We provide services for high-throughput single-cell 3’ mRNA sequencing using nanodroplet-based 10 X Genomics’ platforms. This technology allows flexible cell capture of 500 – 10,000 single cells per sample, with approximately 60% capture efficiency. We also provide 10 X Genomics’ 3’ mRNA-seq analysis for fixed cells where cells are formaldehyde fixed and can be stored up to 3 months before processing. 4 or 16 samples, containing 40 000 – 128 000 cells respectively, can be multiplexed to each sequencing library, making the protocol a good option for bigger projects.

    Sample requirements
    Single-cell suspension from high-viability fresh, frozen or methanol fixed human, mouse, rat, plants and other model organisms can be used for standard 3’ mRNA-sequencing. More detailed instruction for sample requirements can be found from here Fixed RNA profiling kit is compatible with human and soon mouse cells. See more detailed instructions from here. Read more from 10 X Genomics’ webpage

    Epigenomics (scATAC-seq)

    Overview
    Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an analysis method that allows detection of open chromatin sites, such as promoters and regulatory areas, at a whole genome-wide level. We provide 10 x Genomics’ platform for ATAC-seq analysis at a single-cell resolution as well as multiomics application combining ATAC-seq and transcriptome analysis.

    Sample requirements
    Assay is optimized for human and mouse cells. Nuclei suspension from fresh or frozen cells or tissue is needed. See more details from here: 10 X Genomics Single Cell atac & 10 X Genomics’ Chromium Single Cell Multiome ATAC + Gene Expression

    Immune receptor sequencing

    Overview
    We provide 10 X Genomics’ multiomic option for immune profiling. Full length V(D)J segments of B- or T-cell receptors can be analyzed in combination with full transcriptome or gene expression panel to identify for example immune cell clonality, diversity and antigen specificity, on a single-cell level. Cell surface protein analysis of hundreds of different cell surface proteins can be combined to give even more complete picture of immune cell repertoire.

    Sample requirements
    Single-cell suspension of high-viability fresh or frozen human or mouse cells can be used. Cells can be labeled with compatible oligonucleotide barcoded antibodies and/or peptide–MHCs in case cell surface protein detection or antigen binding analysis is of interest. See more detailed instructions from here Read more from 10 X Genomics’ webpage

    Proteogenomics

    Overview
    Single-cell gene expression analysis can be combined with cell surface protein detection using Biolegend’s TotalSeq feature barcoding antibodies. Cells can be stained with oligonucleotide barcoded antibodies or peptides and those oligonucleotide barcodes can be sequenced together with transcriptomes to give a more complete picture of individual cells. Hundreds of different cell surface proteins can be analyzed from a single sample.

    Sample requirements
    High viability, antibody- or peptide-stained cells, should be submitted as aggregate and debris free single-cell suspension. See more detailed instructions from here. Read more from 10 X Genomics’ webpage & more information about Totalseq antibodies and antibody staining protocol

    Spatial Omics

    Spatial Genomics

    Transcriptome-wide gene expression profiling in tissue context

    Overview

    We offer 10 X Genomics’ Visium application and Nanostring’s GeoMx system for spatial transcriptomics analyses. Visium slide has 4 capture areas, each are having around 5000 barcoded spots containing millions of capture oligonucleotides with spatial barcodes unique to each spot. This allows spatial transcriptomics analysis to be performed in whole-genome wide level. On average the resolution of Visium system is 1-10 cells. Nanostring’s GeoMx spatial profiler combines immunofluorescence with optical barcoding technology. Immune pathway and cancer transcriptome probe panels, containing probes for 96 -1800 targets respectively, or whole transcriptome atlas covering ~22 000 transcripts are available. Minimum resolution for small cells e.g. immune cells) is 50-200 cells and large cells (e.g. neurons) is 5-20 cells.[

    Sample requirements

    Visium: Fresh frozen or FFPE samples can be used. 5-35 um thick tissue sections need to be cut and placed onto a Capture Area of specific Visium gene expression slides. Optimal tissue thickness depends on the tissue type, but 10 um is optimal for most tissues. Each slide contains 4 capture areas so 4 different sections can be processed at a time. Link to Visium

    GeoMx: Fresh frozen or FFPE samples can be used. 5-10 um thick sections should be places in the middle of standard SuperFrost™ Plus slides. See more detailed instructions from here Certain steps in the protocol needs to be optimized for each project separately, which should be taken into consideration when planning the project schedule. Link to GeoMx

    Targeted protein profiling

    Overview

    Nanostring’s GeoMx instrument can be used to spatially profile hundreds of proteins simultaneously. Nanostring offers a Human Protein Core panel, containing antibodies against CD45, Ki-67, B2M, CD31 as well as control antibodies. Several different antibody panels, consisting of 10 antibodies each, can be combined to the core panel to increase the number of detectable proteins of interest.

    Sample requirements

    Fresh frozen or FFPE samples can be used. 5-10 um thick sections should be places in the middle of standard SuperFrost™ Plus slides. See more detailed instructions from here Certain steps in the protocol needs to be optimized for each project separately, which should be taken into consideration when planning the project schedule. Link to geomx protein assays

    Mass Cytometry

    Mass Cytometry

    Overview

    Like traditional fluorescence-based flow cytometry, mass cytometry allows multiple cellular parameters to be measured simultaneously. Instead of the in flow cytometry used fluorochromes, mass cytometry uses heavy metal reporter ions. This allows the quantification of up to 45 cellular parameters simultaneously with hardly any overlap. Thus, mass cytometry or cytometry by Time of Flight (CyTOF) adds new dimensions to the study of cellular heterogeneity and diversity. Link to service