GEO DataSets

(Submitter supplied) As an adaptive response to the environment, oaks have evolved long taproots that increase their ability to acquire water. Taproots penetrate deeper layers of soil and send out absorptive roots that can then uptake water from these layers. This ability enables taproots to supply trees with water better. Unfortunately, the applied agrotechnical procedures during seedlings production in container nurseries damage the oaks' taproot, leading to changes in the root system structure. more...

Organism:

Quercus robur

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23233

165 Samples

Download data: FASTA, TSV

(Submitter supplied) Priming of plant defenses provides increased plant protection against herbivores and reduces the allocation costs of defense. Defense priming in woody plants remains obscure, in particular due to plant development traits such as the endogenous rhythmic growth displayed by oaks (Quercus robur). By using bioassays with oak microcuttings, and by combining transcriptomic and metabolomic analyses, we investigated how leaf herbivory by Lymantria dispar and root inoculation with the ectomycorrhizal fungus Piloderma croceum prime oak defenses. more...

Organism:

Quercus robur

Type:

Expression profiling by RT-PCR

Platform:

GPL32604

96 Samples

Download data: TXT

(Submitter supplied) Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability particularly of oak heartwood and, hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. more...

Organism:

Quercus robur

Type:

Methylation profiling by high throughput sequencing; Other

Platform:

GPL27971

19 Samples

Download data: COV

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Tuber magnatum truffles, free-living mycelium and oak mycorrhizal root tips. Paired-end reads of 100 bp were generated and aligned to Tuber magnatum reference transcripts using CLC Genomics Workbench 9.

Organism:

Quercus robur; Tuber magnatum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25294 GPL25295

9 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots. Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.

Organism:

Quercus robur

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23233

9 Samples

Download data: TXT

(Submitter supplied) We describe an application of deep sequencing and de novo assembly of short RNA reads to investigate small interfering (si)RNAs mediated immunity in leaf samples from eight tree taxa naturally occurring in Wytham Woods, Oxfordshire, UK. BLAST search for homologues of contigs in the GenBank identified siRNA populations against a number of RNA viruses and a Ty1-copia retrotransposons in these tree species.

Organism:

Corylus avellana; Quercus robur; Aesculus hippocastanum; Tilia platyphyllos; Fagus sylvatica; Fraxinus excelsior; Betula pendula; Acer pseudoplatanus; Ulmus glabra

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL10477 GPL10476

4 Samples

Download data: TXT

(Submitter supplied) PCR assay Protocol: see manufacturer's website

Organism:

Quercus robur

1 Series

96 Samples

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(Submitter supplied) This platform represents all slides of Series 1, i.e. 1_1, 1_2, 1_3 and 1_4, which are fully identical in their properties except the lot number. PICME Oak 20K 1_2 uses lot number: 17508000(Barcode# 139*); 02508000 (Barcode# 138) PICME Oak 20K 1_3 uses lot number: 17508000(Barcode# 139*); 02508000 (Barcode# 138) PICME Oak 20K 1_4 uses lot number: 07609000 Support: Corning GAPS II/Amplislide Amine (Genewave); Coating: Gamma Amino Propyl Silane Number of spots: 19.968 Number of pins/blocks: 48 Spottdistance in µm: 200 Recurrances spots/slide: 1 Number of spots vertical: 21 Number of spots horinzontal: 20 Vertical offset of first block in µm: 1200 Horizontal offset of first block in µm: 3150 Protocol: Spottingbuffer: 3xSSC+ 1,5MBetain Spottingplate setting: Biozym 10µl Arrayer Hardware: GeneMachines Omnigrid II Arrayer Software: OmniGrid Gridder 2.2.13 Humidity: 50% Dipping time in sec: 1

Organism:

Quercus petraea; Quercus robur

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