Journal: Scientific reports

Article Title: Topological data analysis of pattern formation of human induced pluripotent stem cell colonies.

doi: 10.1038/s41598-025-90592-1

Figure Lengend Snippet: Fig. 2. Artificial induction of exogenous GATA6-HA occurs within the context of endogenous GATA6 expression. (a) Gene circuit for chemical induction of GATA6-HA expression. The pan-GATA6 antibody can detect both induced GATA6-HA and endogenous GATA6 (i.e. the total amount of GATA6), whereas the HA antibody can only detect induced GATA6-HA (i.e. a subset produced via induction of the total amount of GATA6). (b) Representative immunofluorescence images of NANOG and pan-GATA6 or HA at 0 and 25 ng/ml Dox concentrations (scale bar, 440µm). Using Volocity, we applied the gamma changes (gamma of 1.5) after brightness enhancement on all stitched large images used in the figure for better contrast for representation (see Methods). (c) Quantification of segmented images by each channel from (b). Green (NANOG) and red (pan-GATA6 or HA) fluorescent intensities are normalized to the corresponding nuclear Hoechst value in blue. The threshold for the signal in the green channel is given by the green dotted line, and the red dotted line indicates the threshold for the signal in the red channel. The four cell types based on these thresholds are given by the labels R+G−, R+G+, R−G+, and R−G− of the corresponding quadrant.

Article Snippet: Primary antibodies are Nanog (Cell Signaling Technology 4893S, 1:2000), Gata6 (Abcam ab22600, 1:200, R&D Systems AF1700, which was only used in co-staining, 1:200), and HA (Novus Biologicals NB600-363R, 1:200).

Techniques: Expressing, Produced, Immunofluorescence