title: WellWatered_Xylem_rep3
organism: Quercus 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
attributes.tag: ENA first public
attributes.value: 2024-04-29
attributes.tag: External Id
attributes.value: SAMEA114409982
attributes.tag: INSDC center name
attributes.value: ITQB NOVA
attributes.tag: INSDC last update
attributes.value: 2023-09-21T21:22:37Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-13376:WellWatered_Xylem_rep3
attributes.tag: age
attributes.value: 1.5
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: collection date
attributes.value: not collected
attributes.tag: developmental stage
attributes.value: plant tissue development stage
attributes.tag: environmental stress
attributes.value: none (well watered)
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: geographic location (country and/or sea)
attributes.value: not collected
attributes.tag: isolate
attributes.value: not applicable
attributes.tag: organism common name
attributes.value: Cork oak
attributes.tag: organism part
attributes.value: xylem
attributes.tag: replicate
attributes.value: 3
attributes.tag: sample name
attributes.value: E-MTAB-13376:WellWatered_Xylem_rep3
attributes.tag: sampling site
attributes.value: first 10 cm segment of the main stem
attributes.tag: scientific_name
attributes.value: Quercus suber