Biology subjects

Poppe, D.

Publications and source records attributed to Poppe, D..

2 recordsLinked to original sources

bioRxiv2020

Conserved and divergent features of DNA methylation in embryonic stem cell-derived neurons

DNA methylation functions in genome regulation and is implicated in neuronal maturation. Early post-natal accumulation of atypical non-CG methylation (mCH) occurs in neurons of mice and humans, but its precise function remains unknown. Here we investigate mCH deposition in neurons derived from mouse ES-cells in vitro and in cultured primary mouse neurons. We find that both acquire comparable levels of mCH over a similar period as in vivo. In vitro mCH deposition occurs concurrently with a transient increase in Dnmt3a expression, is preceded by expression of the post-mitotic neuronal marker Rbfox3 (NeuN) and is enriched at the nuclear lamina. Despite these similarities, whole genome bisulfite sequencing reveals that mCH patterning in mESC-derived neurons partially differs from in vivo. mESC-derived neurons therefore represent a valuable model system for analyzing the mechanisms and functional consequences of correct and aberrantly deposited CG and non-CG methylation in neuronal maturation.

genomics↗

bioRxiv2019

Systematic bias assessment in solid tissue 10x scRNA-seq workflows

Single-cell and single-nucleus RNA sequencing have been widely adopted in studies of heterogeneous tissues to estimate their cellular composition and obtain transcriptional profiles of individual cells. However, the current fragmentary understanding of artefacts introduced by sample preparation protocols impedes the selection of optimal workflows and compromises data interpretation. To bridge this gap, we compared performance of several workflows applied to adult mouse kidneys. Our study encompasses two tissue dissociation protocols, two cell preservation methods, bulk tissue RNA sequencing, single-cell and three single-nucleus RNA sequencing workflows for the 10x Genomics Chromium platform. These experiments enable a systematic comparison of recovered cell types and their transcriptional profiles across the workflows and highlight protocol-specific biases important for the experimental design and data interpretation.

genomics↗