Single cell Sequencing
MedGenome offers a wide range of single cell sequencing services using the 10X Genomics Chromium system coupled with Illumina HiSeq and NovaSeq next generation sequencing (NGS) platforms.
Single cell sequencing enables the study of sequence information from discrete cells with next generation sequencing (NGS) platforms such as Illumina’s HiSeq, and NovaSeq. For samples that have a heterogeneous microenvironment, this yields a higher resolution understanding of the inherent cellular differences even at low quantity of target DNA/RNA.
Single cell techniques have found various applications that includes detection of DNA mutations, copy-number variants (CNVs), DNA-protein binding, RNA splicing, and the measurement of mRNA expression.
The Chromium system uses 10 X GemCode technology that partitions cells and prepares sequencing libraries in parallel so that all partitions of a particular cell share a common barcode. Upon sequencing, the 10 X Chromium Software can decode the sequence information for each cell using the barcode information.
Example workflow of 10X Genomics system for single cell RNA sequencing
10x GemCode Technology fuels the Chromium System with an innovative reagent delivery system, set of algorithms and turn-key software analysis tools that enable the discovery of previously inaccessible genetic information at massive rate and scale.
Single cell sequencing has applications in:
Cancer sequencing – Single cell sequencing studies help in dissecting the intra-tumour genetic heterogeneity at single cell resolution. Another area where it is showing considerable promise is in Circulating tumour cells (CTCs) – which can be isolated and interrogated as a potential window into the genetics of a tumour through non-invasive sampling.
Metagenomic studies – Single cell genomics approaches greatly helps in renewed understanding of microbial ecology. Specifically, it enhances our understanding of the genomic basis of phenotypic variation between closely related strains, which in turn can be applied for targeted studies of immunogenic bacteria in disease.
Single cell transcriptomics – helps by deciphering the rich information the RNA offers about the phenotype and function of a cell. It examines the level of gene expression in individual cells by simultaneously measuring the messenger RNA (mRNA) concentration of hundreds to thousands of genes. This transcriptomic data will help in mapping all the mammalian organs, tissues and cell types at single cell resolution.
Single cell epigenomics – Epigenetics which is widely studied now based on the correlations made in bulk cell populations is soon changing owing to the increasing evidence of studies indicating how genotypically identical individual cells develop unique phenotypes as a result of unique spatial localization and temporal order. Single cell epigenomics techniques can be combined with RNA expression and SNP data to identify the mechanistic role of epigenetics in gene regulation precisely.
Single cell sequencing in the 10x Genomics system requires a live single cell suspension as the sample input. Cells can be obtained from heterogeneous populations of fresh tissue and fresh or cryopreserved cells. Samples can be prepared from a variety of cell types and animal species, such as human or mouse. Highly viable cells with minimal cellular aggregates is a critical sample requirement in order to accurately capture data from single cells. The platform only requires a small cell sample input, ranging from 500 – 10,000 cells per sample.