GSM9386797: Mock_rep3; Solanum lycopersicum; RNA-Seq
AMF- and mock-inoculated composite tomato cv. Moneymaker plants with roots co-expressing pRolD::mCherry and pSlPT4::GFP were harvested for nuclei extraction at 6 wpi. Per repeat, root sections of a total of 10-12 plants were pooled, in order to obtain a total of approximately 200 mg root material. Harvested root material was placed in the lid of a glass petri dish and chopped intensively in 1 ml of nuclei extraction buffer (NEB; 10 mM MES-KOH pH 7, 10 mM NaCl, 10 mM KCl, 2 mM EDTA, 250 mM mannitol, 0.1 mM spermine, 0.5 mM spermidine, 0.4 u/µl RNase inhibitor - 50:50 mix of Invitrogen SUPERase-InTM and Promega RNAsin Plus) using a razor blade for 1 min on ice, followed by 1 min of incubation. The chopped root material was strained through a 40 µm strainer (pluriSelect), together with 1 additional ml of NEB to collect remaining debris on the petri dish. Nuclei were stained using 40 µl of propidium iodide (PI), and sorted using the BD Biosciences FACSDiscover™ S8 Cell Sorter. Nuclei were centrifuged at 4°C for 10 minutes at 700 g using a swinging bucket rotor, resuspended in nuclei buffer and around 30k nuclei were loaded on a Chromium X Single Cell Instrument (10x Genomics). In the first replicate, the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics) was used, while in the other two replicates the Chromium GEM-X Single Cell 3' Kit v4 was used, both according to the manufacturer's instructions.
GEO
GSM9386797_r1