Detailed Cell-Type Specific Brain Protocols

TRAP data were generated as described (1 (link),2 (link)), and are available for download from GEO: GSE13379. Etv1 data were not plotted because of known contamination with endothelial or lymphoblast cells (1 (link)). Other cell types and drivers are listed in Table 1. This dataset contains samples representing a variety of pure and mixed cell types from different structures of the mouse brain, as well as samples from the corresponding whole tissue. The purified samples are referred to as immunoprecipitates (IP). In parallel, RNA which did not bind to the antibody was also harvested to provide an assessment of the gene expression of the tissue as a whole. These samples are referred to as unbound RNA. Microarray analysis, as traditionally applied to the nervous system, results in samples that are most similar to unbound samples. As the immunoprecipitation does not lead to significant depletion of cell-specific RNAs, here we use the unbound samples as a measure for the total tissue homogenate RNA (referred to as Total).
Table 1.

List of the cell populations, relevant drivers and abbreviations

Cell populations	Driver	Abbreviations used*
Drd1+ medium spiney neurons of neostriatum	Drd1	CS.Drd1
Drd2+ medium spiney neurons of neostriatum	Drd2	CS.Drd2
Cholinergic Interneurons of corpus striatum	Chat	CS.Chat
Motor neurons of brain stem	Chat	BS.Chat
Cholinergic neurons of basal forebrain	Chat	BF.Chat
Mature oligodendrocytes of cerebellum	Cmtm5	Cb.Cmtm5
Astroglia of cerebellum	Aldh1l1	Cb.Aldh1L1
Golgi neurons of cerebellum	Grm2	Cb.Grm2
Unipolar brush cells and Bergman glia of cerebellum	Grp	Cb.Grp
Stellate and basket cells of cerebellum	Lypd6	Cb.Lypd6
Granule cells of cerebellum	Neurod1	Cb.Neurod1
Oligodendroglia of cerebellum	Olig2	Cb.Olig2
Purkinje cells of cerebellum	Pcp2	Cb.Pcp2
Bergman glia and mature oligos. of cerebellum	Sept4	Cb.Sept4
Cck+ neurons of cortex	Cck	Ctx.Cck
Mature oligodendrocytes of cortex	Cmtm5	Ctx.Cmtm5
Cort+ interneurons of cortex	Cort	Ctx.Cort
Astrocytes of cortex	Aldh1l1	Ctx.AldhL1
Corticospinal, corticopontine neurons	Glt25d2	Ctx.Glt25d2
Corticothalamic neurons	Ntsr1	Ctx.Ntsr1
Oligodendroglia of cortex	Olig2	Ctx.Olig2
Pnoc+ neurons of cortex	Pnoc	Ctx.Pnoc
Motor neurons of the spinal cord	Chat	SC.Chat

*Abbreviations used for Figures 4, 5, 7 and Supplementary Figures 7 and 8