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WaterDeficit_Xylem_rep3

Identifiers
BioSample: SAMEA114409973; SRA: ERS16398640
Organism
Quercus suber
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliopsida; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fagales; Fagaceae; Quercus
Attributes
age1.5
collection datenot collected
development stageplant tissue development stage
genotypewild type genotype
geographic locationnot collected
isolatenot applicable
tissuexylem
sample nameE-MTAB-13376:WaterDeficit_Xylem_rep3
ENA first public2024-04-29
ENA-CHECKLISTERC000011
External IdSAMEA114409973
INSDC center nameITQB NOVA
INSDC last update2023-09-21T21:22:37Z
INSDC statuspublic
Submitter IdE-MTAB-13376:WaterDeficit_Xylem_rep3
broker nameArrayExpress
environmental stresswater deficit
organism common nameCork oak
replicate3
sampling sitefirst 10 cm segment of the main stem
scientific_nameQuercus suber
Description

Protocols: Xylem, inner bark (including phloem and cortex), and outer bark (phellem) layers were manually peeled from the first 10 cm segments of the main stem taken above root collar and frozen in liquid nitrogen. Phellem and inner bark layers were collected using the natural breaking regions occurring at the vascular cambium and phellogen, by quickly stripping the full bark layer. Debarked stems were immediately placed in liquid nitrogen and developing xylem was collected by scraping the wood with a scalpel blade. Plants were grown in a glasshouse, in 7 L pots containing a mixture of soil and sand (1:1); well watered plants were treated with 300ml water/day for 18 months; water deficit plants were treated with 300ml water/day for 12 months followed by water witholding for 1 month and 5 months with 300ml water/week. Frozen samples were ground with a mortar and pestle in liquid nitrogen and RNA extraction was performed according to (Reid et al., 2006; DOI:10.1186/1471-2229-6-27) with minor modifications described in (Leal et al., 2022; DOI:10.1093/treephys/tpab176) 1)mRNA enrichment and purification: Oligo dT Selection to enrich the mRNA; 2)RNA fragment and reverse transcription; 3)End repair, add A and adaptor ligation; 4)PCR;5)Single strand separation and cyclization; 6)DNA nanoball synthesis

BioProject
PRJEB66289 The impact of drought on phellem development: morpho-physiological adaptations and gene expression dynamics in cork oak stems
Retrieve all samples from this project

Submission
EBI; 2024-05-01
Accession:
SAMEA114409973
ID:
41147360

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