2025-12-31
ENA first public
ERC000037
ENA-CHECKLIST
CUNI
INSDC center name
public
INSDC status
ERS20917005
SRA accession
AA084-2662-4_AA208-2729-3_M
Submitter Id
21/18 °C day/night
air temperature regimen
2023
collection date
RNA isolated from A. arenosa embryo in the early-torpedo stage.
description
Slovakia
geographic location (country and/or sea)
49.162
DD
geographic location (latitude)
20.15419444
DD
geographic location (longitude)
growth chamber
growth facility
Seeds were surface sterilized with 5% sodium hypochlorite and 0.01% (v/v) of Triton X-100 and planted on Petri dishes with Murashige and Skoog medium (1/2× MS: M0222 Duchefa, 0.8% agar, 10 mM MES, pH 5.8). Planted seeds were stratified for 7 days at 4 °C in the dark and then germinated for 2 weeks at 21/18 °C and 16/8 hours day/night cycle. Seedlings were transferred to soil and cultivated in the same conditions for another 5 weeks. After this, the plants were vernalized for at least two months at 4 °C and 8/16 hours day/night cycle. Vernalized plants were grown under long-day conditions (21/18 °C and 16/8 hours day/night cycle) to induce flowering. Crosses were done by emasculating the maternal plant's unopened flower buds and transferring pollen from the paternal plant 1-3 days after emasculation to the pistil. Siliques were collected 10-16 days after pollination, and endosperm, embryo and seed coat were manually isolated and separated in the developmental stage, varying from early to late torpedo stage, all at room temperature (~24 °C). Siliques were placed on 3M micropore tape, opened by tweezer (Precision tweezers DUMONT® straight with extra fine tips Dumoxel®, 5) and individual seeds were transferred into extraction buffer (0.3 M D(-)-Sorbitol (Millipore®  1.07758), 5 mM MES (DUCHEFA BIOCHEMIE B.V M1503), pH 5.7, filter sterilized). Using the tweezer and insulin syringe (Omnican® 100), individual parts of the seeds were separated. Endosperm and embryo samples originated from 120-160 seeds, and seedcoat samples from 240-320 seeds. Individual fractions were transferred into 2.0 ml safe-lock tubes (Eppendorf 0030123344) and centrifuged for 90 sec at 12,000 g in the bench MiniSpin® centrifuge. Supernatant from all samples was discarded. Endosperm samples were frozen immediately in liquid nitrogen, and embryos and seedcoats were washed two times in 1 ml of extraction buffer before freezing. All samples were kept at -80 °C for further use. RNA was isolated using the RNAqueous™ Total RNA Isolation Kit (Thermo Fisher Scientific) with the inclusion of Plant RNA Isolation Aid (Thermo Fisher Scientific) in the lysis buffer.
isolation and growth condition
16/8 hours day/night
light regimen
Arabidopsis arenosa
organism
PO:0001076
plant developmental stage
soil
plant growth medium
BTO:0001233
plant structure
diploid
ploidy
manual crossing
propagation
Embryos from >240 seeds were separated from endosperm and seedcoat. Seeds were in the early-torpedo development stage. Isolated embryos were frozen in liquid nitrogen and stored at -80°C. RNA was extracted from the frozen sample by RNAqueous™ Total RNA Isolation Kit (AM1912). RNA library and sequencing was done by Novogene company.
sample collection method
healthy
sample health state
early-torpedo embryo stage
sampled age
Arabidopsis arenosa
scientific_name
mother AA084 2662, father AA208 2729 3
source material identifiers
West Carpathian
subspecific genetic lineage name
phylogenetic lineage
subspecific genetic lineage rank
AA_18_19_M
title