Light-Assisted Single-Stranded DNA Open-Chromatin Analysis in Single Spatially Localized Neuronal Cells Identifies the Capacity of Endogenous DNA to Act Catalytically [CHEX-seq]

We report a novel chromatin structure analysis technique, named "CHEX-seq" (CHromatin EXposed), which couples oligonucleotide random annealing and nucleus-resolution photoactivation such that the single-stranded open-chromatin DNA is copied, reverse transcribed, amplified and sequenced. Overall design: We applied CHEX-seq to a variety of cell types and treatments, including K562 cell line culture, cultured human astrocytes and neurons, cultured mouse astrocytes and neurons, and in situ tissue section of mouse neurons. For K562, we performed 12-O-tetradecanoylphorbol-13-acetate (TPA) perturbation and measured by CHEX-seq the single-stranded open-chromatin landscape at pre-treatment, 15min, 1hr, 2hr and 24hr post-treatment. GSM7304391..GSM7304409: NOTE FROM SUBMITTER: we are depositing the raw data files of the human clinical samples to dbGaP