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. 2018 Oct 4;23(4):557–571.e8. doi: 10.1016/j.stem.2018.09.008

Figure 1.

Figure 1

Distinct Gene Expression Programs and Distal Epigenetic Footprints Define Distinct Stages of Astrogliogenesis

(A) Schematic representation of astroglial differentiation from ESCs. Immunofluorescence staining of DAPI and GFAP in the ESC-derived astrocytes during phases of astrogliogenesis, including aNPC, eA, lA_1, and lA_2. Scale bar is 100 μm.

(B) Principal-component analysis plot depicting the distribution of the transcriptomes of ESC (pink), aNPC (light blue), eA (dark blue), and two stages of lA (shades of green) within the scope of the first two components after RNA-seq in these stages. The x and y axes show the percentage of variance explained by the first 2 principal components.

(C) Left side: clustered heatmap depicting the expression of differentially expressed genes during any stage of the in vitro astroglial differentiation, along with the names of known key genes in each of these clusters. Expression in the heatmap is scaled from blue (lowest) to red (highest). Right side: locally weighted scatterplot smoothing (lowess) regression line for these clusters in the same order as the published astrocyte transcriptomes by Cahoy et al. (2008) and Zhang et al. (2016).

(D and E) University of California Santa Cruz (UCSC) browser track example of expression (D) and H3K27ac enrichment (E) at the astroglial genes, i.e., Gfap and Aqp4, and the neuronal gene Rbfox3 during the stages of the in vitro astroglial differentiation (ESC, aNPC, eA, and lA).

(F) Stacked-bar plot depicting the number of common and unique (across astroglial differentiation) H3K27ac peaks under each condition of astroglial differentiation sorted by their genomic location, i.e., intergenic, promoter, exon, and intron.

(G) Venn diagram representing the overlap of the H3K27ac peaks within a distance of 50 kb from the nearest genes called in aNPC, eA, and lA.

(H) Boxplot representing the expression of the genes, as determined as log2-normalized read counts, that are associated with the aNPC, eA, and lA unique H3K27ac peaks depicted in (G).