Source code of the manuscript Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells (bioRxiv).
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report the first single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to mouse embryonic stem cells and embryoid body cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation.
For more details you can read our preprint: https://www.biorxiv.org/content/early/2017/11/10/217554
/preprocessing/: preprocessing scripts/QC/: QC analysis to filter low-quality cells/acc_conservation/: accessibility conservation using clustering of single-cell accessibility profiles/correlations/: pairwise correlations between different omic layers/differential/: differential analysis between subpopulations/dimensionality_reduction/: dimensionality reduction (PCA, t-SNE, ZIFA, etc.)/heatmap/: heatmap plots of the molecular layers/pseudobulk_profiles/: methylation and accessibility profiles using a running window with pseudobulked data/pseudotime/: coupling of molecular layers along a pseudotime trajectory/stats/: calculation of methylation and accessibility statistics (mean, coverage, etc.)/zoom/: plot of zoomed methylation and accessibility values in single genes
The raw data is accessible at GEO (to-do: add link...). The parsed data is provided upon request.
- Computational analysis: Ricard Argelaguet ([email protected]) or Andreas Kapourani ([email protected])
- Experimental protocol: Stephen Clark ([email protected])