I am interested in generating single cell suspensions of brain tissue for downstream use in scRNA-seq. Part of our interests centers on the transcriptomic profile of astrocytes during development and/or inflammatory pathway activation.

We mostly care about differential expression/pathway expression analysis particularly with respect to specific cell populations (e.g. classes of neurons, astrocytes versus microglia, etc).

We want to limit any confounds/experimental noise that might be introduced by the tissue slicing and dissociation process. This can happen rather rapidly:

Article Rapid Manifestation of Reactive Astrogliosis in Acute Hippoc...

Our first thought was maybe flash freezing the tissue and using single nuclei instead of whole cells but we are worried that the sensitivity of our data might degrade too much. Are there other orthodox alternatives to arrest transcription during sample preparation that might be amenable to single cell transcriptomics? Said another way, what might we do to sidestep comparison of 'already reactive' astrocytes in controls versus treatment/conditional groups...