SCExV: a webtool for the analysis and visualisation of single cell qRT-PCR data. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Lang, Stefan; Ugale, Amol; Erlandsson, Eva; Karlsson, Göran; Bryder, David; Soneji, Shamit
• Is Part Of: BMC bioinformatics. Volume 16:Issue 1(2015)
• Page Start: 1
• Page End: 4
• Publication Date: 2015-12
• Subjects: Gene expression -- Single cells -- qRT-PCR -- Webtool -- FACS -- Index sorting -- Visualisation; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-015-0757-z
• Languages: English
• ISSNs: 1471-2105

Abstract

Abstract Background Single cell gene expression assays have become a powerful tool with which to dissect heterogeneous populations. While methods and software exist to interrogate such data, what has been lacking is a unified solution combining analysis and visualisation which is also accessible and intuitive for use by non-bioinformaticians, as well as bioinformaticians. Results We present the Single cell expression visualiser (SCExV), a webtool developed to expedite the analysis of single cell qRT-PCR data. SCExV is able to take any data matrix of Ct values as an input, but can handle files exported by the Fluidigm Biomark platform directly. In addition, SCExV also accepts and automatically integrates cell surface marker intensity values which are measured during index sorting. This allows the user to directly visualise relationships between a single cell gene expression profile and the immunophenotype of the interrogated cell. Conclusions SCExV is a freely available webtool created to import, filter, analyse, and visualise single cell gene expression data whilst being able to simultaneously consider cellular immunophenotype. SCExV is designed to be intuitive to use whilst maintaining advanced functionality and flexibility in how analyses are performed.