Floral transition trajectories dissected by single meristem transcriptomes at high temporal resolution.

We developed a method we denote as single meristem transcriptome profiling (SMT) and utilize it in this work to analyze hundreds of single tomato shoot-apical-meristems of several genotypes, which were collected during or when approaching floral transition. This provide us with dense temporal sampling of the wild-type process which we used in order to generate a pseudo-time reference, anchored by morphology-based scores. This allows for examination of molecular changes in the genetically-perturbed processes by temporal alignment. Prior to RNA extraction from each homogenized meristem, we recorded the number of leaves it produced, and assigned one of five morphological scores to it (describing subtle nuances in meristem doming). UMI-based cDNA libraries were generated from 12-24 technical replicates of each meristem. UMIs from different wells were then summed together to generate one transcriptional profile for each meristem (see quality-control panels for SMT estimates in Meir, Aviezer et al., 2021).