Methods for characterisation of individual cells using a wide range of solutions.
Bulk RNA transcriptomic methods have become very popular and give access to basic gene expression (GE) data on eg. whole tissues. However, any tissue is going to be composed of multiple cell types, and cells with a somewhat different agenda. To really dissect gene expression signals at the cellular level, one will need to look at gene expression at the single cell level.
A number of different methods for single cell expression analysis are available, each with their own advantages and disadvantages. The data you get out may be from the full transcript (eg. Smart-seq) or the 5’ or 3’ ends only (eg. 10X), the platform may be optimised for deep info from each cell (eg. Smart-seq) or for getting you data from the largest possible number of cells (eg. 10X). You may also be happy with standard 10X 3’ GE data, or you may wish to combine it with other “omics” (eg 10X ATACseq, cell surface markers, etc). Finally, the sequencing depth and the optimal scale to plan for - these will depend on what you are after.
NGI currently offers single-cell sequencing using the Smart-seq3 and 10X Genomics platforms, but we are also continually evaluating new methods and protocols.
Profiling of gene expression levels at single-cell resolution.
library preparation transcriptomics single cell illumina rnaseq smartseq3 SS3 single-cellSingle-cell profiling of gene expression levels on fixed cells.
fixed cells library preparation transcriptomics single cell RNA mRNA illumina RNA-Seq chromium 10x GenomicsProfiling of gene expression levels at single-cell resolution.
illumina RNA-Seq chromium 10x Genomics library preparation transcriptomics single cell RNA mRNAProfiling of chromatin accessibility at the single cell level.
chromium chromatin 10x Genomics ATAC library preparation epigenetics single cell illumina ATAC-seq dnaProfiling of 3´gene expression and chromatin accessibility in the same cell.
single cell RNA mRNA illumina ATAC-seq RNA-Seq ATAC chromium library preparation 10x Genomics transcriptomicsCombining short & long reads at the single cell level.
chromium 10x Genomics full transcript library preparation single cell long-read illumina ontSingle-cell profiling of gene expression levels on a large number of cells.
RNA-Seq parse library preparation transcriptomics single cell RNA mRNA illumina