Single cell Epigenomics

Single cell epigenomics is the study of the epigenome at the single cell level. It allows to study for example chromatin compaction and histone marks in each individual cell and to make a direct correlation with gene expression levels. The epigenetic heterogeneity within a population of cells can thus be assessed, and rare epigenetic events can be identified. The single cell initiative proposes several approaches:

 

Single cell ATAC-seq

Single Cell ATAC-seq, in which ATAC stands for “Assay for Transposase Accessible Chromatin”, allows to measure chromatin accessibility at the single cell level. The assay relies on the transposase Tn5, which cuts accessible chromatin regions and loads NGS adapters on the DNA fragments for subsequent sequencing. Single cell ATAC-seq provides insights into cell types and states, as well as gene regulatory mechanisms.

 

Single cell ATAC-seq at the NGS platform

Single cell ATAC-seq is available at the NGS platform using the 10X Genomics solution. The required input material is 1,000 to 20,000 nuclei and the recovery rate (yield) is around 50% of loaded nuclei. The sequencing recommendations are around 25k reads per nucleus.

 

 

 

Single cell ChIP-seq

Single Cell Chromatin ImmunoPrecipitation (ChIP) allows to determine at the single cell level how specific chromatin marks are distributed across the genome. Marks associated with actively transcribed chromatin, such as H3 lysine 4 trimethylation (H3K4me3), or associated with gene repression, such as H3 lysine 27 trimethylation (H3K27me3) can be mapped in each cell and provide information about cell types and states, chromatin organization and gene expression regulation.

 

Single cell ChIP-seq at the Custom Single Cell Omics platform

The Custom Single Cell Omics platform develops single cell ChIP-seq for H3K4me3 and H3K27me3 on fresh samples (cell lines and PDXs) using microfluidics and DNA barcoding. The required starting material is at least 200,000 cells in order to sequence around 3,000 cells. More to come soon.

 

 

Combined scATACseq/RNA-seq

Combined scATACseq/RNA-seq allows to simultaneously profile gene expression and open chromatin regions, and thus to integrate two complementary layers of (epi)genomic information in each single cell. It thus provides a powerful tool to correlate chromatin accessibility with gene expression.

 

Combined scATAC-seq/RNA-seq at the NGS platform

Combined sc ATAC-seq/RNA-seq is available at the NGS platform using the 10X Genomics solution. The required input material is 1,000 to 20,000 nuclei and the recovery rate (yield) is around 50% of loaded nuclei. The sequencing requirements are aound 25k read pairs per nucleus.