Cell type- and transcription-independent spatial proximity between enhancers and promoters

Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell type-specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. These images were processed to identify nuclei and the loci within them. The shared dataset is composed of spot positions for promoter and enhancer probes in individual cells. It is comprised of 14 separate files, each corresponding to an individual plate imaged on a different day. Column headers and contents are consi..., DNA FISH
High-throughput fluorescence in-situ hybridization was performed as described previously (Finn and Misteli 2021). Probes were generated from Bacterial Artificial Chromosomes (BACs) containing target regions. Bacteria from a single colony was grown into a large-scale culture and target DNA was purified via alkaline lysis using the Nucleobond BAC 100 Maxiprep kit (from Takara). DNA was then quantified and stored at -20°C for future use. Probes were generated from BAC DNA by a nick translation reaction incubated at 16°C for 1 hr 20 min with the following mix: 40 ng/uL DNA, 0.05 M Tris-HCl pH 8.0, 5 mM MgCl2, 0.05 mg/ml BSA, 0.05 mM dNTPs with all dTTP replaced with fluorescently labeled dUTP, 1 mM β-mercaptoethanol, 0.5 U/μL E. coli DNA Polymerase and 0.5 μg/μL DNAse I. The reaction was stopped with the addition of 1 μL EDTA per 50 μL reaction volume and heat shocked to 72°C for 10 min, then stored at −20°C overnight. QC gels were run in 2% agarose to verify successful nick transl..., , # Data from: Cell type- and transcription-independent spatial proximity between enhancers and promoters

[https://doi.org/10.5061/dryad.6t1g1jx5v](https://doi.org/10.5061/dryad.6t1g1jx5v)

This dataset consists of 2D spot positions generated from maximum intensity projections of images of high-throughput fluorescence in situ hybridization experiments. The data consists of identifying information (experimental date, filename, well, field, cell, and spot indices), position information (x, y, and radial positions), and metadata information (information on probes and cell types used).

## Description of the data and file structure

High-throughput DNA FISH was performed in a 384-well plate format. Automated imaging was performed in three channels (405, 488, and 561 nm excitation lasers) on a CV8000 dual spinning disc confocal microscope with a 60X water immersion lens (NA = 1.2) and no pixel binning for a final pixel size of 108 nm. Maximum intensity projections were performed at the time o...