EPI-CyTOF-Brain

Epigenetic mechanisms regulate gene expression programs during neurogenesis, but the extend of epigenetic remodelling during human cortical development remains unknown. Here, we characterize the epigenetic landscape of the human developing neocortex by leveraging Epi-CyTOF, a mass cytometry-based approach for the simultaneous single cell analysis of more than 30 epigenetic marks.
Conclusion:
This study comprehensively characterized the epigenetic state of specific neural cell types and identified the histone modification H3K27me3, deposited by the Polycomb Repressive Complex 2 (PRC2), as the modification with the strongest cell type-specificity during human developing neocortex.
Notes:
Within this exploratory data set, human foetal tissue (gestation week 12?14) and human cortical organoids (culture week 8) derived from two independent induced pluripotent stem cell (iPSC) lines were stained with a brain-specific EPI-CyTOF antibody panel consisting of 10 cell type markers and 31 histone modifications or epigenetic regulating enzymes. To reduce batch effects each tissue was analyzed in four replicates and analyzed as pool after palladium-based barcoding with the suspension mass cytometer CyTOF XT. To standardize the measurements with the CyTOF XT, a daily tuning was performed before measurement. All antibodies were tested and titrated before usage. Samples were individually barcoded with the Cell-ID 20-Plex Pd Barcoding Kit (Standard BioTools, PN 201060), stained with one batch of a pre-prepared and frozen antibody master mix, and were aquired as pool with 10% EQ™ Six Element Calibration Beads (Standard BioTools, PN 201245). During analysis, the automated detector voltage feature ensured stable measurements over time.