ArticlebioRxiv : the preprint server for biology2026
MipSScs: Artificial neural network-based data integration of 2D/3D single-cell spatial RNA sequence data from virus-infected human cerebral organoids.
Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
There is interest in the use of recent single-cell spatial transcriptomic technologies to gain biological insights into disease mechanisms. Previously, we characterized the use of herpes simplex virus 1 (HSV-1) induced neuroinflammation in 2D dissociated cells from human cerebral organoids (dcOrgs) to model molecular and transcriptomic readouts associated with Alzheimer's disease (AD). In this work, we generated two datasets by using single-cell non-spatial RNA sequencing and single-cell spatial RNA sequencing technologies on HSV-1-infected 2D dcOrgs and HSV-1-infected 3D cerebral organoids (cOrgs). We conducted cell type assignment for the cells in the 2D dcOrgs and 3D cOrgs, by using single-cell non-spatial RNA sequence data from human fetal brains and adult post-mortem brains, to infer the transcriptomic effects of AD-associated
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