Journal: bioRxiv
Article Title: BeadBuddy: user-friendly, nanometer-scale registration of single-molecule imaging data
doi: 10.1101/2025.11.25.690467
Figure Lengend Snippet: a) In vitro adipogenesis model. Mesenchymal stromal cells (MSCs) were plated and cultured in either regular or differentiation medium for indicated durations. b) Representative image of PPARG RNA FISH in undifferentiated MSCs (Day 0) and adipocytes (Day 14). c) Proportion of nuclei exhibiting bursts of transcription on one (monoallelic) or two of the alleles (biallelic) across four timepoints. d) Left: number of transcript-intensity equivalents per burst at each active transcription site. Right: total number of nuclear transcripts per nucleus. * P < 0.05, ** P <0.01. *** P <0.001. e) Top: H3K27ac ChIP-seq tracks of the PPARG locus during adipogenic differentiation (range: 0-30 for all tracks); bottom: Genomic target regions labeled by DNA FISH in four colors. f) Representative maximum intensity projection of DNA FISH data (downstream control locus not shown). g) Pairwise 3D distances between genomic regions of interest measured by DNA FISH and corrected using BeadBuddy. Empirical cumulative distribution functions visualizing changes in distance between specified genomic elements as a function of differentiation timepoint (average of two technical replicates for each timepoint). h) Spatial density heatmaps: each datapoint is an absolute distance of the promoter from the midpoint of the two enhancers on that promoter’s allele. Green and purple ovals represent a distribution of enhancer positions relative to the midpoint (the origin) where each oval’s long axis is 1 standard deviation of enhancer distance from the midpoint. Detailed Statistics are presented in Supplementary Table 1.
Article Snippet: Human mesenchymal stromal cells (hMSCs, ATCC: PCS-500-011) were cultured in Dulbecco’s modified Eagle’s medium with Glutamax (DMEM, Thermo: 10-569-044) supplemented with 10% FBS (Avantor Seradigm, VWR 1500-500) and 1X penicillin-streptomycin (pen/strep) (Thermo Scientific 15140122) during expansion and for the undifferentiated condition.
Techniques: In Vitro, Cell Culture, ChIP-sequencing, Labeling, Control, Standard Deviation