2024-11-29
ENA first public
ERC000011
ENA-CHECKLIST
HMGU
INSDC center name
public
INSDC status
ERS20128822
SRA accession
E-MTAB-14123:Shoot_ctrl_rep1
Submitter Id
2
year
age
ArrayExpress
broker name
not collected
collection date
date palm
common name
Khalas
cultivar
Protocols: Harvested plant material of both experiments (total leaves, whole roots) was immediately cut into small pieces, homogenized in liquid nitrogen to fine powder and stored at -80°C until further analyses. About two years old seedlings of micro-propagated Phoenix dactylifera, cultivar Khalas were purchased from Date Palm Developments Ltd. (Somerset, U.K.). Seedlings were planted in 5-L pots filled with 70% quartz gravel (3 – 5 mm diameter, Quarzwerke GmbH, Frechen, Germany) and covered by 4 cm soil substrate (Floragard Vertriebs-GmbH, Oldenburg, Germany). For the drought stress experiment, plants were transferred into walk-in phytotrons at the Research Unit of Environmental Simulation (EUS; Helmholtz Center Munich, Neuherberg, Germany), to simulate climatic conditions of the date palm's natural habitat (12 h:12 h, light:dark; 40:20 °C; approx. 5:30% humidity, 600 μmol photons m-2 s-1 at shoot height) as described elsewhere (Du et al. 2023). Each plant was automatically irrigated by 50 ml of tap water every 4 hours. After 2 weeks of acclimation, water deprivation treatment was initiated by withholding watering for 3 days and then supplying 50 ml de-ionized water per day. Soil water contents were measured using a ML2 ThetaProbe connected to a HH2 moisture meter (Delta-T, Cambridge, UK). Soil moisture throughout the experiment was kept at 21.4 ± 7.5% and 10.7 ± 5.2% for control and water deprivation, respectively. RNA isolation for RNAseq was done as described in Paoletti et al. 2021. At the Biomedicum Functional Genomics Unit (FuGU, Helsinki, Finland), the shoot total RNA was ribo-depleted using ribo-zero rRNA removal (Plant leaf) (Illumina) and the root total RNA was ribo-depleted using ribo-zero rRNA removal (Plant Seed/Root) (Illumina). The total RNA input amounts used for ribo-depletion were 200 ng for shoot and 1 µg for root. The NEBnext ultra directional (polyA purification) Kit was used for library construction.
description
LP.04 four leaves visible stage
developmental stage
wild type genotype
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Phoenix dactylifera
organism
Phoenix dactylifera
organism
shoot
organism part
Phoenix dactylifera
scientific_name
control
stimulus
Shoot_ctrl_rep1
title