Journal: Nature Communications

Article Title: Joint single-cell DNA accessibility and protein epitope profiling reveals environmental regulation of epigenomic heterogeneity

doi: 10.1038/s41467-018-07115-y

Figure Lengend Snippet: Epigenetic variability is modulated by the hypoxic microenvironment. a FACS sorted EpCAM+ and HIF1α+ double-positive cells from the same mouse breast tumor; three groups of HIF1α staining were assigned, HIF1α negative ( n = 762), HIF1α low ( n = 139), HIF1α high ( n = 55) (right plot). b Ranking of transcription factor motif variability of different HIF1α-staining groups, HIF1α negative ( n = 702), HIF1α low ( n = 95), HIF1α high ( n = 42). c Examples of TF motif deviations, which significantly change in HIF1α high group compared with the others. In each comparison, HIF1α negative ( n = 702), HIF1α low ( n = 95), HIF1α high ( n = 42). Significance of Wilcoxon test shown with n.s. (not significant), * p < 0.05 and ** p < 0.01. d Flow cytometry analysis of HIF1α protein abundance in 4T1 breast cancer cells cultured in 5% oxygen (Ctrl, gray) or 1% oxygen for indicated time points. e Chromatin accessibility changes of hypoxic conditions compared with control. Red indicates higher, blue lower accessibility. f TF deviation examples of motifs whose accessibility increases in hypoxia over time in 4T1 breast cancer cells (TF deviation was calculated using ChromVAR)

Article Snippet: In all, 1×10 6 cells isolated from a PyMT mouse breast tumor (see above) were stained for 30 min at room temperature for rat anti-mouse EpCAM-BV421 (BD Horizon, #563214), HIF1α-PE (R&D, #IC1935P), CD45-Alexa488 (BioLegend #103122, clone 30-F11), followed by donkey anti-rabbit 488 secondary antibody.

Techniques: Staining, Flow Cytometry, Cell Culture