Tools are available for cell-type specific transcriptome analysis in rodents, including isolation of cell types for culture and isolation of live cell types using FACS sorting or antibody-specific beads. Isolations of mouse brain cell types (e.g. astrocytes, microglia, endothelial cells) have been used to create databases of cell-type specific transcriptomes in several brain regions. Bioinformatics analyses of cell types have identified thousands of cell-type enriched genes and splicing isoforms (Zhang et al., 2014b). These databases can be applied to existing and future datasets to identify novel markers for cell identification, tools for genetic manipulation, and insights into disease states. FACS sorting has similarly been used to create databases of cell-type specific transcriptomes. For example, a novel Tmem119 antibody and FACS-sorted microglia RNA-seq revealed the expression of novel ligands, receptors, and disease-associated genes. This strongly suggested new microglial functions in immune effector functions, regulation of catecholamines, and synapse formation (Bennett et al., 2016). FACS sorting was also used to determine cell-type specific changes after LPS administration, revealing that LPS-altered genes in certain cell types were not found in whole tissue preparations
