SVZ Cell Atlas

SVZapp is developed by the Rajewsky lab at the Berlin Institute for Medical Systems Biology of the Max Delbrück Center in Berlin.

Vera Zywitza, Aristotelis Misios, Lena Bunatyan, Thomas E. Willnow , and Nikolaus Rajewsky

Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NSCs are crucial for regulating stem cell self-renewal and differentiation. We used single-cell RNA profiling to generate an unbiased molecular atlas of all cell types in the largest neurogenic niche of the adult mouse brain, the subventricular zone (SVZ). We characterized > 20 neural and non-neural cell types and gained insights into the dynamics of neurogenesis by predicting future cell states based on computational analysis of RNA kinetics. Furthermore, we apply our single-cell approach to mice lacking LRP2, an endocytic receptor required for SVZ maintenance. The number of NSCs and proliferating progenitors was significantly reduced. Moreover, Wnt and BMP4 signaling was perturbed. We provide a valuable resource for adult neurogenesis, insights into SVZ neurogenesis regulation by LRP2, and a proof-of-principle demonstrating the power of single-cell RNA-seq in pinpointing neural cell type-specific functions in loss-of-function models.

About the App:

This web app accompanies Dataset A of the manuscript. In the first tab (All Cells) the expression of individual genes can be explored and visualised in 9,804 single cells derived from the adult SVZ. The second tab (Neurogenic Lineage) contains the subclustering analysis of NSCs, TAPs, and NBs and provides higher resolution of the neurogenic lineage.

Normalized UMI counts are plotted in both the violin and feature plots. They were calculated by dividing the UMI counts of each gene per cell by the total number of UMIs of the corresponding cell, multiplying the value by 10,000 and applying the logarithmic transformation. Genes that are not detected are excluded from the drop-down list.

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All Cells

NSCs: neural stem cells; TAPs: transient amplifying progenitors; NBs: neuroblasts; OPCs: oligodendrocyte progenitor cells; COPs: differentiation-committed oligodendrocyte precursors; MFOLs: myelin forming oligodendrocytes; MOLs: mature oligodendrocytes; SMCs: smooth muscle cells; PVMs: perivascular macrophages; MSNs: medium spiny neurons.

Neurogenic Lineage

Subclustering analysis of NSCs, TAPs and NBs.