Single Cell mRNA Sequencing

    We provide a service for high-throughput 3´-single-cell mRNA sequencing using the nanodroplet-based Chromium™ Controller from 10x Genomics. The resulting sequencing libraries are compatible with Illumina sequencing platforms.

    Description of the Technique

    1. Construction of Single Cell Libraries with the Chromium 10x Genomics

    • Encapsulation of the cells

    Single cell are encapsulated with gel beads and master mix. Primers with Unique Molecular Identifier (UMI), or “barcode” are linked to the gel beads.

    • Cell lysis and RT PCR, taking place inside each GEM (Gel Bead in Emulsion)
    • Pooling for cDNA amplification and library construction in bulk. The libraries are indexed and can be multiplexed if necessary





    Final library construct

    Key features :

    • Throughput of up to 10,000 single cells per sample.
    • Theoretical multiplet rate ranges from 0.4% of 500 recovered cells to 7.6% of 10,000 recovered cells.
    • 1-8 samples can be processed in parallel.

    2. Sequencing of the Single Cell Libraries

    The following platform, available in-house at the FFGC core, can be used for the sequencing of single cell libraries.

    • Hiseq 3000 (High Output)
    • Hiseq 2500 (High Output and Rapid Run)
    • Miseq

    3. Data Analysis with 10x Genomics Software

    Sequencing data is processed and aligned using the CellRanger pipeline from 10x Genomics. The following files are provided to the user:

    A plethora of tools for scRNA-seq data analysis has been developed. An extensive listing of these can be found at
    Bespoke analysis service is available through the Medical Bioinformatics Centre.


    Sample Requirements

    • Samples can be either freshly prepared or viable frozen cells.
    • No data can be recorded from dead or apoptotic cells. Presence of such cells in the sample will decrease the number of cells detected by the analysis and might compromise data quality.
    • The nominal cell capture efficiency is about 60%, but we highly recommend starting with at least 50,000 cells.
    • The protocol is compatible with cell sorting and MACS purification.
    • Cells from solid tissues can be analysed, provided that the dissociation process does not compromise viability.
    • The samples must be in a single-cell suspension, without aggregates, excess debris or contaminants.
    • We recommend adhering to sample preparation protocols provided by 10x Genomics.