characteristics.text: 2026-01-01
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Department Molecular Genetics
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS27078052
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-15759:L401HPKH21P01S3IC
characteristics.characteristic: Submitter Id
characteristics.text: SAMEA115475503
characteristics.characteristic: biosamples identifier
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: rape
characteristics.characteristic: common name
characteristics.text: Express 617
characteristics.characteristic: cultivar
characteristics.text: 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.
characteristics.characteristic: description
characteristics.text: stage 3 (mid storage)
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.characteristic: genotype
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Brassica napus
characteristics.characteristic: organism
characteristics.text: Brassica napus
characteristics.characteristic: organism
characteristics.text: inner cotyledon
characteristics.characteristic: organism part
characteristics.text: Brassica napus
characteristics.characteristic: scientific_name
characteristics.text: L401HPKH21P01S3IC
characteristics.characteristic: title