DS.02.01 E. nindensis MOA-seq protocol and plant sampling conditions

INTRODUCTION This dataset provides the protocol for Eragrostis nindensis (E. nindensis) plant growth conditions, drought stress, rehydration and sampling strategies is based on previous protocols developed in Jill Farrant’s lab at the University of Cape Town[1],[2]. The protocol describing the preparation of nuclei followed by digestion with micrococcal nuclease I (MNAse I) and the preparation of libraries refers to the protocol originally developed for maize[3] and its subsequent optimization in Dr. Thomas Hartwig’s lab, Independent Research Groups, Max Planck Institute for Plant Breeding Research, Cologne, and Institute for Molecular Physiology, Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany. The figures showing nuclei digestions results are derived from the experiments, conducted by Giuseppe Trotta, University of Dusseldorf, Germany and Bojana Banovic Deri, CREA-CI, Italy, in collaboration with Sohini Mukherjee and Sergius Weize,l University of Dusseldorf, in Thomas Hartwig’s lab, Max Planck Institute for Plant Breeding Research, Cologne, Germany. The bioinformatic analysis of the E. nindensis data has been optimized starting from the methodology initially developed for maize, as for the wet-lab protocol. The pipeline ranges from the quality control of raw reads to peak calling and differential peak calling. [1] https://www.mdpi.com/2223-7747/14/4/531 [2]https://www.researchgate.net/publication/225279941_Physiological_response_of_selected_Eragrostis_species_to_water-deficit_stress [3] https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009689