L401HPKH21P01S2OC
Brassica napus
Protocols: Developing seeds were sampled at five stages of seed development (stage 1 = pre-storage, stage 2 = early storage, stage 3 = mid storage, stage 4 = late storage, stage 5 = maturation). From stage 2 onwards, seeds were manually dissected into four separate organs/tissues (SC = seed coat, IC = inner cotyledon, OC = outer cotyledon, and RA = radicle). Three biological replicates per stage x organ combination were generated, comprise pools of dissected seed material from multiple individual siliques and different plants. Depending on the developmental stage (seed size), between two hundred and five hundred individual seeds were sampled, dissected, and pooled per biological replicate to provide sufficient material (a minimum of approx. 100 mg) for subsequent molecular omics analyses. All samples were snap frozen in liquid nitrogen directly after dissection of the respective seed and stored at -80 °C until RNA extraction. Plants were grown in the container-based system of the PhenoSphere at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) under controlled environmental conditions in 2020-2021. In each container 48 plants were grown (sowing density: 48 plants/m2). Containers were filled with 1 m3 soil, divided into layers simulating natural soil layers: top soil from the field, loam, coarse sand, and coarse gravel. The climate regime was based on twelve years of hourly records (between 2008 and 2019) from IPK's weather station, and designed to simulate a representative growing season with a dynamic field-like environment, including the simulation of wind and diurnal changes. Plants were watered by an automatic drip irrigation system. During the winter months (November to March), containers were moved outside the facility for hibernation, providing natural cold (negative) temperatures. Small RNA was extracted from sample (15-20 mg aliquot of pooled seed tissue) using the miRNeasy Kit (Qiagen, Venlo, The Netherlands, Cat. No. 217084), according to the manufacturer's instructions, to enrich for microRNAs (miRNAs) and other small RNA molecules < 200 nt. Library generation and sequencing was  performed by GenXPro (GenXPro GmbH, Frankfurt Main, Germany). Small RNA libraries were prepared with the TrueQuant Small RNA Seq Kit (GenXPro) according to the manual of the manufacturer. The small RNA molecules were ligated with 3'- and 5'-adapters containing unique molecular identifiers (UMIs), reverse transcribed, followed by PCR amplification with a minimal number of cycles, and silica-bead purification.
ENA first public
2026-01-01
INSDC center name
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department Molecular Genetics
INSDC status
public
Submitter Id
E-MTAB-15759:L401HPKH21P01S2OC
biosamples identifier
SAMEA115475494
broker name
ArrayExpress
collection date
not collected
common name
rape
cultivar
Express 617
developmental stage
stage 2 (early storage)
genotype
wild type genotype
geographic location (country and/or sea)
not collected
isolate
not applicable
organism part
outer cotyledon
sample name
E-MTAB-15759:L401HPKH21P01S2OC
scientific_name
Brassica napus