10X Genomics single cell Chromium

10X Genomics workflow

                                                                                                              Modified from https://www.10xgenomics.com/technology/

The Chromium Single Cell 3′ platform is now available with the BRC Genomics Facility. The system provides a comprehensive, scalable solution for single cell genomics profiling of thousands of cells  with each preparation. Up to 8 independent samples can be quickly processed in parallel. The instrument uses microfluidics technology to generate an emulsion in which droplets encapsulate a cell and reagents. Barcoded oligos are used in each droplet to assign a cell-specific tag to each captured mRNA molecule. The cDNA produced is used to generate a 3'end RNA library for Illumina sequencing. After sequencing, the cell-specific barcodes are used to separate the reads on a per-cell fashion, additional unique molecular identifiers (UMI) are used to remove PCR duplicates.  

tSNE plot

10X Genomics' Loupe Cell Browser can be freely downloaded to visualise data files and: 

Identify genes that uniquely characterize clusters

- Locate different cell types and functional groups based on gene expression

- Create new clusters and dissect your data in even smaller subgroups

Save genes of interest, export data tables, and capture screenshots of your single-cell data



Example of a report showing number of cells detected, number of reads and genes per cell.

Additional metrics are shown including sequence saturation, and data quality.