Skip to main content
Fig. 1 | Genome Biology

Fig. 1

From: ATRX regulates glial identity and the tumor microenvironment in IDH-mutant glioma

Fig. 1

A single-cell chromatin atlas of IDH-mutant glioma. A Overview of the analysis of human clinical specimens. B Summary of the scATAC-seq data and separation of neoplastic cells. C PCA and clustering of neoplastic cells from the scATAC-seq data, based on genome-wide open-chromatin signatures. The first two PCA components are hierarchically clustered via Pearson correlation as a metric and Ward’s linkage. D Transcription-factor motif frequencies in scATAC-seq data for select motifs that are differentially enriched between IDH-A and IDH-O neoplastic cells at q<0.05 (Table 3), assessed via ChromVAR, represented as standardized deviances from expected (Methods), and separated by cluster. Error bars represent standard error. E Average expression (top) and log2 fold-change between IDH-A and IDH-O (bottom) for stem-like neoplastic cells, restricted to gene sets previously implicated during neuronal and glial genesis, assessed via limma (Additional file 3: Table S2 and Additional file 4: Table S3). The percentages of each cell-type’s gene set that are differentially expressed in IDH-A vs. IDH-O stem-like cells are represented as word clouds below. The higher the percentage, the larger the word

Back to article page