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. Author manuscript; available in PMC: 2021 Mar 7.
Published in final edited form as: Nat Neurosci. 2015 Nov 2;18(12):1819–31. doi: 10.1038/nn.4160

Figure 1. Comparison of proteome and RNA-Seq data.

Figure 1

(a) Graphical illustration of the workflow for the cell type– and brain structure-resolved mouse brain proteome. DIV, days in vitro. (b) A bar chart showing number of proteins identified in adult mouse brain and each of the cultured cell type with FDR of 1% when analyzed as 6x SAX fractions. CGN, cerebellar granule neurons. (c) A total of 10,529 proteins were identified in all cell types and brain (∼84% of all identified proteins) and an average of ∼99% protein identifications were shared between at least two proteomes. (d) Single run analysis of the mouse brain, the different brain structures and the developing cerebellum; four biological replicates (triplicates for optic nerve and corpus callosum) were measured by single 4-h LC MS/MS runs.Numbers of identified proteins are indicated after matching between runs with fractionated brain and cell-type proteome runs in the MaxQuant environment. (e) RNA-Seq analysis of cultured cells and resulting density plots of gene expression levels. The density estimates of gene expression levels are shown for each cell type and for a combination over all cell types as indicated. The combined cell type was derived by extracting the largest expression value over all cell types. In all cell types, gene expression levels followed a binomial distribution (black). Geneexpression filtered for RPKM > 1 values are shown in blue. (f) Venn diagram of the number of expressed genes on the mRNA level and on the protein level.