AA_1_2_E
Arabidopsis arenosa
RNA isolated from A. arenosa endosperm in the early-torpedo stage of the embryo.
ENA first public
2025-12-31
INSDC center name
CUNI
INSDC status
public
Submitter Id
AA208-2727_AA084-2657_E
air temperature regimen
21/18 °C day/night
collection date
2022
geographic location (country and/or sea)
Slovakia
geographic location (latitude)
49.043514
geographic location (longitude)
20.180772
growth facility
growth chamber
isolation and growth condition
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.
light regimen
16/8 hours day/night
plant developmental stage
PO:0001076
plant growth medium
soil
plant structure
BTO:0000390
ploidy
diploid
propagation
manual crossing
sample collection method
Endosperm from >120 seeds was separated from embryo and seadcoat. Seeds were in the early-torpedo development stage. Isolated endosperm was frozen in liquid nitrogen and stored in -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 health state
healthy
sample name
AA208-2727_AA084-2657_E
sampled age
early-torpedo embryo stage
scientific_name
Arabidopsis arenosa
source material identifiers
mother AA208 2727, father AA084 2657
subspecific genetic lineage name
West Carpathian
subspecific genetic lineage rank
phylogenetic lineage