Fig. 1: Comparison of astrocyte transcriptomes in vivo and in vitro and between human and mouse.
a An astrocyte bound to an anti-HepaCAM antibody-coated petri dish during immunopanning purification. RNA was extracted immediately after the cells stuck to the dish. These samples are referred to as acutely purified. Scale bar: 10 μm. b Astrocytes in serum-free culture stained with anti-GFAP antibodies. Scale bar: 50 μm. c A bright-field image of an astrocyte in serum-free culture. Scale bar: 20 μm. d Expression of reactive astrocyte marker genes in serum-selected and serum-free cultures of human astrocytes. Z-score is calculated as (RPKM—average RPKM across all samples)/standard deviation. Genes with FDR < 0.1 between serum-selected and serum-free cultures and RPKM > 1.5 are shown. e, f Scatter plots and Spearman’s correlation coefficients (ρ) of gene expression between cultured and acutely purified human astrocytes using the serum-selected culture method and our serum-free culture method. For each condition, gene expression across 3–5 patient samples was averaged. Only protein-coding genes were included. Two-tailed t-test. p < 2.2×10−16. g Scatter plot and Spearman’s correlation of gene expression between acutely purified human and mouse astrocytes. Two-tailed t-test. p < 2.2×10−16. Human brain tissue was derived from donors of different ages (8–63 years). Mouse brain tissue was derived from postnatal and adult mice. Additional information is provided in Supplementary Data 8. h Number of genes with similar or species-dependent expression. Genes with percentile rankings in the top two-thirds were included in this analysis to eliminate those not expressed or expressed at very low levels. Percentile rankings of the expression of each gene were compared across human and mouse astrocyte samples and differences were tested by Welch’s T-test followed by post-hoc multiple comparison adjustment using the Benjamini and Hochberg FDR method124–126. FDR < 0.05. i, j Protein interaction networks of genes expressed at higher levels by mouse astrocytes than human astrocytes (i) and at higher levels by human astrocytes than mouse astrocytes (j) (percentile ranking difference > 0.4). FDR < 0.05. Blue: genes associated with the GO term metabolism. Green: genes associated with the cellular component mitochondria. Red: genes associated with the GO term defense response. Yellow: genes associated with the cellular component extracellular.
