In Tabula Muris we used a random forest model strategy to identify sets of transcription factors using FACS and droplet data that can potentially be used to inform the design of novel reprogramming protocols.
“Technical confounders” are likely correlated with real biology. Regressing them out can badly distort the data.
In the Tabula Muris study, we performed single-cell RNA sequencing on tissues from multiple mice using two different technologies: microfluidic droplet-based 3’-end counting on the 10x genomics platform, and FACS-based full-length transcript analysis with Smart-Seq2. Both platforms have advantages: droplets let us easily profile thousands of cells while Smart-Seq2 recovers more genes per cell and provides full-length transcripts.
The Chan Zuckerberg Biohub recently released Tabula Muris, a compendium of single cell transcriptome data from the mouse containing nearly 100,000 cells from 20 organs and tissues. The data allow for direct and controlled comparison of gene expression in cell types shared between tissues, such as immune cells from distinct anatomical locations. They also allow for a comparison of two distinct technical approaches:
As an organization devoted to bringing together researchers and sharing knowledge, it is high time that the Chan Zuckerberg Biohub had a blog. So here it is. Tune in for updates on our many projects and news about new technologies.