Astrocyte-enriched murine cortical and white matter transcriptional profiles after stroke in spatially-defined zones of post-stroke reactivity

Zones of reactive astrocytes after stroke were defined in both white matter and cortical stroke models using a combination of phenotyping and morphology. These zones were then excised via laser capture microscopy in mGFAP-77.6-Cre/Ribotag mice and astrocytic ribosomes were immunopreciptated to generate astrocyte-enriched zone-specific transcriptomic profiles. RNA extracted from cleared lysate (input) was used to assess astrocytic enrichment in white matter and cortex in both the uninjured brain and in the combined first three zones of reactivity after stroke, comparing expression profiles to matched immunoprecipitated ribosome-associated RNA. Overall design: Enrichment cohorts: uninjured white matter and uninjured cortex, both cleared lysate (input) RNA and ribosomally-associated immunoprecipitated RNA (IP), 5 per group. Post-stroke zones 1-3 white matter and cortex, both cleared lysate (input) RNA and ribosomally-associated immunoprecipitated RNA (IP), 3 per group. To assess enrichment, IP samples were compared to input from the same cohort. Astrocyte-enriched post-stroke samples: IP samples from each of 5 zones per stroke model and their respective uninjured control (also used in enrichment analyses); 4-5 samples per zone. To assess stroke-induced changes in gene expression, each post-stroke zone was compared to the uninjured samples from that brain region.