May 23 , 16:00 - 16:15

Nextflow allows Pixelgen innovation engine to reach the market quicker

Molecular Pixelation (MPX) is a technology that facilitates the study of relative location of proteins on the cell surface of single cells by NGS readout. During our talk we will introduce how this is possible using MPX and Pixelator, our dedicated software which we have developed within Pixelgen Technologies to generate data for protein abundance, spatial polarizaty and colocalization of proteins. We will also demonstrate how we use our Nextflow pipeline, nf-core/pixelator, to orchestrate data processing for customers and our internal R&D team. In our publication, we demonstrate how DNA-oligo tagged antibodies coupled to DNA-pixels are used to assess proteins on the cell surface. We determine the relative location of these proteins by creating neighborhoods that are uniquely identifiable and interconnecting them in a two-step workflow. Based on the information readout, we build an in-silico graph that allows us to get information about abundance and relative location of constellations of proteins for 1000 cells simultaneously. Pixelator is a software that transforms raw sequencing data into ready-for-analysis PXL files that can be analyzed with our data science tools in R and Python. To our knowledge, we are the first company to open-source our pipeline as part of the nf-core initiative and in this talk, we will try to demonstrate how this has benefited our customers and our core innovation engine.
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Johan Dahlberg, Florian De Temmerman, Ludvig Larsson, Max Karlsson, Vincent van Hoef, Pouria Tajvar, Stefan Petkov