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Single Cell Seminars (May): Unsupervised mapping for scRNA-seq; Joint profiling of chromatin accessibility & more

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If you have a question about this talk, please contact Dr Lia Chappell.

At the Genome Campus (Hinxton), but we look forward to welcoming colleagues from Cambridge too!

Note: Non-campus people should email LC5 so that you can be signed in as a visitor at reception. Please do this before 2.30pm on the day, thanks!

Please come along to the second of the rebooted monthly campus Single Cell Seminar series. This month we have two exciting talks, one wet lab and one dry lab.

1) Vladimir Kiselev (Sanger): scmap – A tool for unsupervised mapping of single cell RNA -seq data to a reference database

2) Stephen Clark (Babraham Institute: Joint profiling of chromatin accessibility, DNA methylation and transcription in single cells

Vlad’s talk: scRNA-seq allows for de novo identification of cell-types. There are currently plans for building a human cell atlas that will serve as a reference for all of the cell types found in the human body. One of the most important uses of such an atlas will be for comparison of new experiments – e.g. asking if the cells found in a disease sample are present in the healthy reference. In addition to learning about which known cell-type a given cell corresponds to, a particularly important question is whether or not a cell represents a new class which is not present in the reference. I will present scmap – a tool for fast and accurate projection of cells to a reference database for scRNA-seq data. We validate scmap on several publicly available datasets collected from different platforms and labs. We also show that scmap is scalable and can be used with a reference database consisting of millions of cells.

Stephen’s talk: Technical advances enabling DNA accessibility measurements in single cells have characterised heterogeneity in a number of cell types but the transcriptional consequences of this variability are unclear. We recently demonstrated the utility of parallel single-cell sequencing to reveal novel links between epigenetic features, such as DNA methylation, and gene expression. Here we build upon our method by introducing an in vitro GpC methylase step to mark regions of accessible chromatin prior to RNA capture and bisulfite sequencing; mapping genome-wide chromatin organisation, endogenous CpG methylation and transcription from the same single cell. Using single-cell methylase accessibility, we are able to profile a larger proportion of the genome than published ATAC -seq and DNAse-seq methods. The ability to map closed chromatin (GpC unmethylated) as well as open chromatin (GpC methylated) increases confidence in the data and the presence of multiple GpC sites within a given region gives sufficient resolution to discern nucleosome positions in single cells. We apply our method to pluripotent mouse ES cells, measuring heterogeneity in all three molecular layers which we leverage to discover correlations and infer novel relationships, revealing strong and widespread associations between chromatin accessibility and DNA methylation.

This talk is part of the Single Cell seminars at the Wellcome Genome Campus series.

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