Integrated single-nucleus RNA-seq dataset of mouse brain from a multi-factorial benchmarking study

Here we present the first multi-factorial benchmarking study of snRNA-seq technical confounders in the adult mouse brain, by performing a systematic evaluation of tissue harvest methods (post-mortem vs. in vivo) and nuclear fixation (methanol-fixed vs. fresh), using the identical sequencing platforms (SeekOne Digital Droplet).

We find that standard post-mortem harvest induces a rapid, selective loss of metabolically active glutamatergic neuron subpopulations, which obscures transcripts related to advanced cognitive functions while preserving overall cellular proportions. While methanol fixation minimally alters cell-type composition, it introduces cell-type-specific gene expression shifts that preferentially stabilize structural and core functional transcripts.