GSE128680
Multiscale gene expression profiling of 1 cm root tips of control and submerged Oryza sativa, Medicago truncatula, Solanum lycopersicum and Solanum pennellii seedlings
Climate change has increased the frequency and intensity of floods that impact global agricultural productivity. To better understand the response mechanisms and evolutionary history of gene family member regulation across angiosperm phyla, we studied the rapid submergence response of rice, the legume Medicago truncatula, and two Solanum species, domesticated tomato (S. lycopersicum cv. M82) and its dryland-adapted wild relative S. pennellii. Response to hypoxic conditions was measured by analyzing transcriptional and post-translational regulation in root tips of each species. This was achieved by the use of Nuclei Tagged in specific Cell Types (INTACT) and Translating Ribosome Affinity Purification to obtain chromatin and sub-populations of gene transcripts. (1) Chromatin accessibility was evaluated by coupling INTACT with ATAC-seq (assay for Transposon-Accessible Chromatin). (2) INTACT was used to capture nuclear RNA (nRNA). (3) Polyadenylated mRNA (polyA RNA) was obtained by standard oligo(dT) selection. (4)  Ribosome-associated polyA mRNA (polyA RNA) was obtained by use of Translating Ribosome Affinity Purification (TRAP).  Ribosome footprinting (Ribo-seq) was accomplished by using TRAP to capture ribosome protected fragments after RNAseI digestion. Samples evaluated include the apical root tip (four species) and shoot region (Solanum species only) under control conditions and after 2 h of submergence Overall design: 5 genotypes (Oryza sativa, Medicago truncatula-hairy root, Solanum lycopersicum, Solanum lycopersicum-hairy root and Solanum pennellii ), 2 conditions (control and 2 hour-submerged tissue grown on petri dishes with 1X MS, 1 % [w/v] Sucrose, pH 5.8). 4 bioreplicates of 4 RNA pools (total mRNA, rRNA degraded nuclear RNA, TRAP-RNA, Riboseq-RNA) and ATAC-seq. Up to two tissues (root tip and shoot apical meristem). Please note that [1] the Sample titles indicate RNA population tissue and species as following: INRNA: Nuclear RNA TOT: Poly A RNA TRA: Polysomal PolyA RNA RS: Ribo-seq RNA OS: Oryza Sativa MT: Medicago truncatula SL: Solanum lycopersicum M82 SP: Solanum pennellii ROOT: 1 cm root tip SHOOT: Shoot apex [2] The processed data generated from multiple samples is linked as Series supplementary files and is inidicated in the corresponding sample description field.