library_construction_protocol: An RNAqueous® Total RNA Isolation Kit (ThermoScientific) was used to isolate total RNA from the IZE explants induced on different media (E0, EA, ET) for 5 and 10 days. The freshly isolated tissues were wiped in frozen mortars. Depending on the age of the culture, from 250 (5th day) to 100 (10th day) explants were used for RNA isolation per repetition. RNA isolation, library preparation, and sequencing were produced in three biological replicates. The concentration and purity of RNA samples were evaluated with an ND-1000 spectrophotometer (NanoDrop Technologies). The integrity of the RNA was determined using an Agilent 2100 Bioanalyzer and Agilent RNA 6000 Nano chips (Agilent Technologies, Santa Clara, USA). RNA samples were treated with RNase-Free DNase and then purified using the Acid-Phenol: Chloroform with ammonium acetate method (ThermoScientific). The sequencing libraries were prepared using Illumina ScriptSeq™ Complete Kit (Plant; Illumina, San Diego, USA) following the manufacturer's protocol. Two micrograms of total RNA per sample were used as an input. Briefly, library prep involved the subsequent steps: ribosomal RNA removal with Ribo-Zero rRNA Removal Reagents (Plant Leaf; Illumina, San Diego, USA) followed by ethanol precipitation of the rRNA-depleted sample, RNA fragmentation, cDNA synthesis, RNA removal, terminal tagging of cDNA followed by bead cleanup, PCR amplification using Illumina indexes and final bead purification. The quality of the prepared Illumina libraries was analyzed using Agilent Bioanalyzer with the Agilent High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, USA), and the quantities were estimated using a Qubit Fluorometer (Thermo Fisher Scientific, Waltham, USA). For cluster generation, the libraries were pooled with equimolar concentration and sequenced using the Illumina HiSeq 4000 system (Illumina, San Diego, USA) in 2x 76 cycles paired-end (PE) mode with 6 barcoded samples per lane.