title: Illumina NovaSeq 6000 paired end sequencing; Transcriptomic response of grafted tomato seedlings leaves after root inoculations with rhizobacteria Azospirillum brasiliensis and Paraburkholderia graminis
design: Transcriptomic response of grafted tomato seedlings leaves after root inoculations with rhizobacteria Azospirillum brasiliensis and Paraburkholderia graminis
library_construction_protocol: Leaf samples were harvested at flowering stage, 35 days after inoculations, from three plants for each treatment (control, inoculated with AB, inoculated with PG), frozen in liquid nitrogen and stored at −80 °C Two weeks after grafting, seedlings were transplanted in pots (6.5 cm x 8.0 cm x 5.5 cm) filled with neutral peat (23% organic carbon, 0.5% nitrogen, pH 6, electrical conductivity 0.25 dS m-1, and dry apparent density 214 kg m-3; Dueemme S.r.l., Reggio Emilia, Italy). After inoculations, seedlings were grown in a growth chamber located at the University of Modena and Reggio Emilia (Reggio Emilia, Italy) with a photoperiod of 16 h light and 8 h dark and the day/night temperatures of 25/19°C. Seedlings were watered every two days with 50 mL of water per pot. Compo BIO fluid stillage (organic nitrogen 3%, potassium oxide 6% and organic carbon 10%, COMPO ITALIA S.R.L (Cesano Maderno, Italy) was added to the irrigation water (10 mL L-1) once a week for two weeks. A fully randomized experimental design with ten biological replicates per treatment were adopted. Immediately after transplanting, bacterial treatments with Azospirillum brasiliensis sp.245 (AB) and Paraburkholderia graminis C4D1M (PG), belonging to CREA GB's collection, were performed by adding 1 mL of inoculum (107 colony forming unit (CFU) mL-1) close to the seedlings's root collars  Frozen samples were pulverized in a sterile mortar using liquid nitrogen, and the total RNAs were extracted from ground tissues using Nucleospin® RNA plant kit (Macherey–Nagel, Duren, Germany) according to manufacturer instructions, and eluted in 60 µL of RNase-free water The nine high-quality RNA samples were sent in dry ice to Novogene company (UK sequencing centre, Cambridge) for libraries construction