Source code of the manuscript Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells.
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
/serum_cells/: analysis done on ~100 embryonic stem cells under serum conditions/EB_cells/: analysis done on ~50 embryoid body cells
The raw data is accessible at GEO GSE109262. Parsed data is provided upon request.
- Computational analysis: Ricard Argelaguet ([email protected]) or Andreas Kapourani ([email protected])
- Experimental protocol: Stephen Clark ([email protected])
We have created a Slack group to discuss ideas, suggestions and collaborations about scNMT-seq. This is the link, feel free to join and talk to us!