title: a10
organism: Solanum tuberosum
description: Protocols: Plants were removed from the media and the roots aseptically removed from the leafy part. Roots were rinsed in sterile distilled water before flash freezing in liquid nitrogen. Uninoculated plant controls were sampled in parallel. Before nucleic acid extraction, root tissue was ground in liquid nitrogen. Radish (Raphanus sativus L. var. oleiformis Pers. cv. Bento) seeds were surface sterilised in 2% calcium hypochlorite solution (10ml) before germination on distilled water agar (0.5% w/v) in the dark for 5-7 days, at ~20C. Potato (Solanum tuberosum var. Estima) microplants (Gentech Propagation, UK) were cut at the internode, transplanted onto Murashige and Skoog (MS; Merck) + 20% (w/v) sucrose (MS20) agar and incubated for 14 days to establish new microplants. Seedlings, or microplants, were transplanted into 175ml pots (Greiner, UK) containing autoclaved perlite and sterile 0.5 x MS liquid medium. Seedlings were grown 16 h light/ 8h dark photoperiod for a further seven (potato) or 21 days (radish) at ~20C before Pectobacterium atrosepticum SCRI1039 inoculation. Treatments ended after 14 days. Each biological sample pooled the roots from three radish or two potato plants. Total RNA was extracted using Macharey-Nagel Nucleospin RNA Plant kit, following manufacturers guidelines with RAP buffer. Samples were treated with Turbo DNase-free kit (Invitrogen, AM1906) to remove gDNA carryover. RNA quality was checked with Agilent Bioanalyzer 2100 following supplier´s instructions Library construction was completed by Novogene.150bp paired end Illumina library
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2024-01-17T00:28:37Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2024-01-17T00:28:37Z
attributes.tag: External Id
attributes.value: SAMEA114498699
attributes.tag: INSDC center name
attributes.value: Information and Computational Sciences The James Hutton Institute
attributes.tag: INSDC first public
attributes.value: 2024-01-17T00:28:37Z
attributes.tag: INSDC last update
attributes.value: 2024-01-17T00:28:37Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13434:a10
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: collection date
attributes.value: not collected
attributes.tag: common name
attributes.value: potato
attributes.tag: cultivar
attributes.value: Estima
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: infect
attributes.value: none
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism part
attributes.value: root
attributes.tag: sample name
attributes.value: E-MTAB-13434:a10
attributes.tag: scientific_name
attributes.value: Solanum tuberosum