2024-03-07
ENA first public
ERC000011
ENA-CHECKLIST
SAMEA114518088
External Id
Department of Agriculture, Food, Environment and Forestry (DAGRI) University of Florence
INSDC center name
2023-10-19T14:34:00Z
INSDC last update
public
INSDC status
ERS16499433
SRA accession
E-MTAB-13465:RC1
Submitter Id
4
month
age
ArrayExpress
broker name
not collected
collection date
apple
common name
Roho
cultivar
Protocols: Peels of three randomly selected fruits for each experimental condition (‘Ariane’ control fruits (AC); ‘Ariane’ fruits inoculated with N. vagabunda showing no symptoms (AI); ‘Roho’ control fruits (RC); ‘Roho’ fruits inoculated with N. vagabunda showing no symptoms (RI); diseased ‘Roho’ fruits (RD)) were sampled for RNA extraction and immediately frozen in liquid nitrogen. Since apple fruits were the vegetal material used for the experiment, we didn’t use any growth protocol. ‘Ariane’ and ‘Roho’ fruits were harvested at commercial ripening stage in an orchard belonging to the Edmund Mach Foundation, located in Trentino region in northern Italy (latitude 46.179766°, longitude 11.117726°). After harvest, fruits were artificially inoculated by spraying an inoculum of N. vagabunda. For inoculum preparation, the isolate CBS102871 of N. vagabunda was grown in tomato agar (Cameldi et al. 2017) and incubated in the dark at 15°C. After 21 days, conidial suspension was prepared by scraping mycelium, suspending it in sterile deionized water and adjusting to the final concentration (105 conidia ml-1). Fruits were stored at 4 °C with a relative humidity of 95% for 4 months. Fruit peel was sampled and immediately frozen in liquid nitrogen. Total RNA was extracted from apple peel using the Spectrum plant total RNA kit (Sigma-Aldrich, St. Louis, MO, USA), according to the manufacturer’s instructions, including the on-column DNase digestion step. In order to assess the integrity of the genetic material, 1 µl of RNA was loaded onto 1.5% agarose gel. RNA was then quantified using Nanodrop 8000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Libraries were prepared with NEBNext® Ultra™ RNA Library Prep Kit (New England BioLab) by integrating Illumina unique dual index adapters (Illumina).
description
fruit ripening stage
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
none
infect
not applicable
isolate
Malus domestica
organism
Malus domestica
organism
fruit peel
organism part
wild type
phenotype
Malus domestica
scientific_name
RC1
title