2025-05-21
ENA first public
ERC000011
ENA-CHECKLIST
Wageningen University, Plant Physiology group
INSDC center name
public
INSDC status
ERS24440942
SRA accession
E-MTAB-15125:Sample 13
Submitter Id
4
day
age
ArrayExpress
broker name
not collected
collection date
thale cress
common name
Col-0
cultivar
Protocols: Detached roots were harvested in dark conditions using a green safe-light and immediately frozen in liquid nitrogen. Each sample comprised material from 40 roots, which were stored at -80 °C until RNA extraction. seeds were surface-sterilised and then sowed on 1/10th Murashige and Skoog medium including vitamins (Duchefa Biochemie), supplemented with 0.5 g/ l MES (Duchefa Biochemie) and 0.8% Diashin Agar (Duchefa Biochemie), pH5.8. After 3-4 days of stratification in dark at 4˚C, plates with seed were then placed vertically at 90˚ in a growth chamber for 3 days in white light (100µE, 16h photoperiod, 20˚C) to stimulate germination. At day 3, roots were detached and placed on the same media, supplemented with 5 mM sucrose (Duchefa Biochemie) unless otherwise stated. For osmotic stress and ABA treatments, the medium was additionally supplemented with 25 mM sorbitol (Duchefa Biochemie), 25 mM mannitol (Duchefa Biochemie), 12.5 mM NaCl (Duchefa Biochemie) or 30 nM ABA (Duchefa Biochemie) unless otherwise stated. Root tip position was marked after detachment, and roots were grown in darkness for another 4 days at either 20˚C or 28˚C.  seeds were surface-sterilised and then sowed on 1/10th Murashige and Skoog medium including vitamins (Duchefa Biochemie), supplemented with 0.5 g/ l MES (Duchefa Biochemie) and 0.8% Diashin Agar (Duchefa Biochemie), pH5.8. After 3-4 days of stratification in dark at 4˚C, plates with seed were then placed vertically at 90˚ in a growth chamber for 3 days in white light (100µE, 16h photoperiod, 20˚C) to stimulate germination. At day 3, roots were detached and placed on the same media, supplemented with 5 mM sucrose (Duchefa Biochemie) unless otherwise stated. For osmotic stress and ABA treatments, the medium was additionally supplemented with 25 mM sorbitol (Duchefa Biochemie), 25 mM mannitol (Duchefa Biochemie), 12.5 mM NaCl (Duchefa Biochemie) or 30 nM ABA (Duchefa Biochemie) unless otherwise stated. Root tip position was marked after detachment, and roots were grown in darkness for another 4 days at either 20˚C or 28˚C.  Samples were ground in Retsch shaker mill with two 1/8” metal ball bearings per sample, at a frequency of 25 Hz for 30 seconds twice. Total RNA was extracted using RNeasy Plant Mini kit (Qiagen), according to manufacturer instructions. RNA poly-A enrichment library preparation were carried out by Novogene.
description
seedling developmental stage
developmental stage
snrk2.2/snrk2.3
genotype
not collected
geographic location (country and/or sea)
not applicable
isolate
Arabidopsis thaliana
organism
Arabidopsis thaliana
organism
root
organism part
Arabidopsis thaliana
scientific_name
20 degree
stimulus
Sample 13
title