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 regulate stem cell self-renewal and differentiation. We used comprehensive and untargeted single-cell RNA profiling to generate a molecular cell atlas of the largest germinal region 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 applied our single-cell approach to document decreased numbers of NSCs, reduced proliferation activity of progenitors, and perturbations in Wnt and BMP signaling pathways in mice lacking LRP2, an endocytic receptor required for SVZ maintenance. Our data provide a valuable resource to study adult neurogenesis and a proof-of-principle for the power of single-cell RNA-sequencing to elucidate neural cell type-specific alterations 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.