QuRIE-seq_manuscript

Abstract

Current high-throughput single-cell multi-omics methods cannot concurrently map changes in (phospho)protein levels and the associated gene expression profiles. We present QuRIE-seq (Quantification of RNA and Intracellular Epitopes by sequencing) and use multi-factor omics analysis (MOFA+) to map signal transduction over multiple timescales. We demonstrate that QuRIE-seq can trace the activation of the B-cell receptor pathway at the minute and hour time-scale and provide insight into the mechanism of action of an inhibitory drug Ibrutinib.

In this repository

Folder structure

Build using workflowr project.

A nice html-page that is generated from the Rmd files in the analysis folder can be accessed here

To run the Rmd files: 1) clone the repository. 2) Download the raw count tables from GSE162461 and save in data/raw/ folder. 3) First run the QC.Rmd file. After that either MOFAaIg or MOFAibru Rmd files can be used.

Github page

The docs folder contains the actual github page.

Three pages contain code to process, analyse and create figures:

• QC processes count tables (available at GSE162461: filter high quality cells; normalize and scale counts.
• MOFA aIg computes a model of cells stimulates with aIg molecule.
• MOFA ibru computes a model of cells stimulates with aIg molecule with or without prescence of ibrutinib.