BioInfoRx and Biogen have developed scRNASequest, an open-source ecosystem for scRNA-seq analysis, visualization, and publishing. To make this powerful pipeline more accessible, our team has introduced a fully supported and user-friendly version in BxGenomics, enabling academic and small biotech researchers to leverage its capabilities without the need for extensive IT and bioinformatics expertise. Here we shared some tips we learned from developing and running the pipeline on hundreds of scRNA-Seq experiments.
The oncoprotein SET can bind to p53 and inhibits p53 transcriptional activity in unstressed cells. To identify the genes regulated by SET in a p53-dependent manner, the endogenous SET was depleted by siRNA in control or p53 knockout U2OS cells. We use BxGenomics DEG and Venn Diagram tools to find genes regulated by p53-SET.
Reference: Nature. 2016 Oct 6;538(7623):118-122. doi: 10.1038/nature19759.
We use BxGenomics to examine RNA-Seq data from three key time points during human iPSC differentiation into mature muscle fibers with motor neurons. We can detect consistent genes changes as the cells differentiate, and myogenesis and nurogenesis genes are highly enriched in later time points.
Reference: Cells. 2020 Jun 23;9(6):1531. doi: 10.3390/cells9061531.