Single Cell Profiling of Chromatin Accessibility in Cotton Ovule Epidermis Durring Early Fiber Development [scATAC-seq]

Each cotton seed has approximately 25,000 singular fiber cells, which account for 25-30% epidermal cells. Understanding the basis of fiber cell initiation is critical for cotton yield improvement. However, it is difficult to separate and study fiber and non-fiber cells. Here we developed a reliable single-cell protocol to study chromatin accessiblity in fiber and epidermal cells of developing ovules. We analyzed over 4,000 nuclei derived predominately from the epidermal layer of ovules during early stages of fiber development. Overall design: Whole ovules of Gossypium were collected and briefly digested using macerozyme and cellulase enzyme mix to release protoplasts from the epidermal surrface, including developing fiber cells. Ovules from Gossypium hirsutum TM1 at 0, 1 and 2 days post-anthesis, The protoplasts were purified using differential gradient centrifugation, lysed, and nuclei were then isolated and analyzed using via 10x scATAC sequencing.