Expanding the scope of multimodal single cell sequencing

Aims

Multimodal single cell sequencing in the form of 10x Genomics’s new paired single cell RNA/ATAC assay kit is poised to re-revolutionise the field of single cell genomics. The assay allows the simulations analysis of a cell’s transcriptional out and its underlying chromatin architecture. As part of this project we will establish and innovate new workflows to considerable expand the scope of this exciting new technology.

Aim 1: To establish a sample multiplexing workflow

Aim 2: To establish a Perturb-seq approach for the multimodal assay kit.

Aim 3: To generate a new multimodal single cell workflow for the simultaneous detection of a DNA interacting protein of choice and cell surface proteins.

Brief project outline

10x Genomics’s new paired single cell RNA/ATAC assay has the potential to unravel complex biological phenomena by enabling paired transcriptional and epigenetic profiling. In order for this exciting new technology to achieve its full potential, this proposal will implement a workflow for sample multiplexing via antibody based indexing of nuclei, and establish a robust analysis pipeline for sample demultiplexing of the sequencing data. Furthermore, we will adapt a recent technique developed for single cell RNAseq to generate a separate sequencing library for lentiviral transcripts to allow the robust detection of lentiviral “perturbations” in the context of small or larger scale factor screens. Lastly the project will innovate a new kind of multiomic assay by using the underlying architecture of the new 10x multimodal assay kit. The assay can be done with permeabilised cells (and not nuclei), to not only allow detection of histone marks in the genome but also the presence of proteins on their cell surface.

Genomics-based innovative aspect of proposal

Each aim of this project will establish a new workflow that, as of now, has not yet been developed in connection with the new 10x genomics single cell multimodal assay.

Broad applicability of the technique

Like for traditional single cell RNA sequencing the potential applications are broad. To help with uptake we will make the developed computational pipelines available through the GIH (and/or Github) and are happy to support other groups in their endeavours to perform lentiviral screens as well as provide support and advise for upstream sample processing for the multiomic assay.