github link
Accession IconSRP170960

Bulk RNA-seq of adult homeostatic microglia from 4 brain regions

Organism Icon Mus musculus
Sample Icon 12 Downloadable Samples
Technology Badge IconNextSeq 500

Submitter Supplied Information

To compare microglial regional heterogeneity, we generated bulk RNA-seq profiles of postnatal day 60 microglia, sorted by TMEM119+ (also CD45lowCD11b+), from cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR) regions. For each sample, 3000 microglia were FACS sorted into RLT lysis buffer for total RNA extraction, followed by Smart-seq library preparation and Illumina Nextseq (sequence depth 10-20 million per sample). Consistent with our scRNA-seq data, samples from 4 regions were highly correlated (R>0.99), and individual samples did not cluster according to tissue origins, suggesting striking similarities between homeostatic microglia from different brain regions. Moreover, we could not detect any differentially expressed genes (FDR < 0.05) between regions from the bulk samples. These data suggest that classical adult microglia with homeostatic signatures (e.g. Tmem119), as the most dominant microglial population in the healthy brain, have little transcriptomic heterogeneity across brain regions. Overall design: TMEM119+ microglia (3000 cells each sample) from a given region were FACS sorted from pooled male animal samples (C57BL/6N) into RLT lysis buffer in Eppendorf tubes. Three replicates were done for each region. Libraries were prepared following the Smart-seq protocol (v4 ultra low input RNA kit). All samples were barcoded and pooled together for Illumina Nextseq sequencing.
PubMed ID
Total Samples
Submitter’s Institution
No associated institution
Alternate Accession IDs


Show of 0 Total Samples
Accession Code
Specimen part
Cell line
Processing Information
Additional Metadata
No rows found