GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Quercus glauca; Lithocarpus edulis

Type:

Expression profiling by array

Platforms:

GPL32572 GPL32573

144 Samples

Download data: TXT

(Submitter supplied) In the family Fagaceae, fertilization is delayed by several weeks to more than one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year of flowering. Although delayed fertilization was recorded over a century ago, underlying mechanisms remain to be explored. To uncover the key genes associated with delayed fertilization, we obtain and analyze the comparative molecular phenology data over two years in one-year (Quercus glauca) and two-year fruiting species (Lithocarpus edulis). more...

Organism:

Quercus glauca

Type:

Expression profiling by array

Platform:

GPL32573

72 Samples

Download data: TXT

(Submitter supplied) In the family Fagaceae, fertilization is delayed by several weeks to more than one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year of flowering. Although delayed fertilization was recorded over a century ago, underlying mechanisms remain to be explored. To uncover the key genes associated with delayed fertilization, we obtain and analyze the comparative molecular phenology data over two years in one-year (Quercus glauca) and two-year fruiting species (Lithocarpus edulis).

Organism:

Lithocarpus edulis

Type:

Expression profiling by array

Platform:

GPL32572

72 Samples

Download data: TXT

(Submitter supplied) Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. more...

Organism:

Quercus robur

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33794

27 Samples

Download data: TXT

(Submitter supplied) The periderm is basic for land plants due to its protective role during radial growth, which is achieved by the polymers deposited in the cell walls. Despite the research on the topic has unravelled the role of several enzymes and transcription factors, many questions remain open, especially those regarding cell development. Here we use the outer bark of cork oak (cork), holm oak (rhytidome), and their natural hybrids’ to further understand the mechanisms underlying periderm development. more...

Organism:

Quercus suber; Quercus x morisii; Quercus ilex

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33234 GPL33232 GPL33233

16 Samples

Download data: XLSX

(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) The periderm is a protective barrier crucial for land plants survival, but genetic factors involved in its regulation are fairly unknown. In a previous transcriptomic approach in the cork oak periderm (Quercus suber) we identified a RS2-INTERACTING KH PROTEIN (RIK) homolog, of unknown function and with a K homology (KH)-domain RNA-binding protein, as a regulatory candidate gene in the periderm. To gain insight into the function of RIK in periderm, the potato (Solanum tuberosum) tuber periderm was used as a model. more...

Organism:

Solanum tuberosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16436

12 Samples

Download data: CSV

(Submitter supplied) The phellogen or cork cambium is a bifacial stem cell population from which derivatives are formed by periclinal divisions and specified on opposing sides as phelloderm (inwardly) and phellem or cork (outwardly). Altogether the three layers constitute the periderm which covers and protects the radially-grown organs (stems, roots and tubers) and wounded tissues from dehydration and pathogen attack. The phellem is the final responsible of the protective function of periderm and despite its vital importance, just the suberin biosynthetic process has been studied molecularly while other processes are poorly understood. more...

Organism:

Quercus suber

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28954

11 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Quercus lobata

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL30178 GPL27543

9 Samples

Download data: TSV

(Submitter supplied) STAR aligned RNA-seq reads were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

Organism:

Quercus lobata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27543

3 Samples

Download data: WIG

(Submitter supplied) Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

Organism:

Quercus lobata

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30178

3 Samples

Download data

(Submitter supplied) WGBS sequencing of Valley Oak bud, catkin and leaf tissues

Organism:

Quercus lobata

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL27543

3 Samples

Download data: TSV

(Submitter supplied) Background: Prevention of hyperlipidemia and associated diseases is a health priority. Complementary medicine based on scientific evidence has recently recognized the potential of natural products for modulating lipid metabolism, such as the medicinal mushroom Ganoderma lucidum (Gl), which possesses hypocholesterolemic, prebiotic and antidiabetic properties. Methods: Whole-transcriptomic changes in liver and kidney from a mouse model (C57BL/6), under a high-cholesterol diet and standardized Gl extracts (Gl-1, Gl-2) or simvastatin administration, were analyzed to determine Gl hypocholesterolemic activity. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

45 Samples

Download data: CEL, TXT

(Submitter supplied) Transcript profiling of leaves from Quercus ilex seedlings subjected to well-watering and drought-stress (irrigation withdrawal) conditions

Organism:

Quercus ilex

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28136

12 Samples

Download data: FA, 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) Reforestation is effective in restoring ecosystem functions and enhancing ecosystem services of degraded land. The three most commonly employed reforestation methods of natural reforestation, artificial reforestation with native Masson pine (Pinus massoniana Lamb.), and introduced slash pine (Pinus elliottii Engelm.) plantations were equally successful in biomass yield in southern China. However, it is not known if soil ecosystem functions, such as nitrogen (N) cycling, are also successfully restored. more...

Organism:

Bacteria; Viruses; Archaea; Fungi

Type:

Genome variation profiling by array

Platform:

GPL23836

42 Samples

Download data: XLSX

(Submitter supplied) Epigenetic modifications, such as DNA methylation where methyl groups are added to cytosine base pairs, have the potential to impact phenotypic variation and gene expression, and could influence the ability of plants to respond to changing environmental conditions. One approach to determining the association between DNA methylation, phenotypic variation, and gene expression, is through the application of chemical demethylation agents, such as 5-Azacytidine, which inhibit DNA methylation and lead to a partial reduction in DNA methylation across the genome. more...

Organism:

Quercus lobata

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27543

12 Samples

Download data: CSV

(Submitter supplied) Purpose: The goal of this study is to provided a comprehensive genomic information for functional genomic studies in Q. mongolica. Methods:The Quercus mongolica leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. more...

Organism:

Quercus mongolica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26114

1 Sample

Download data: FASTA, TXT

(Submitter supplied) Purpose: The goal of this study is to screen the candidate genes involved in drought avoidance of Q. liaotungensis Methods:The Q. liaotungensis leaves were generated by deep sequencing, using Illumina Hiseq 4000. The high-quality reads were obtained by removing the reads that contained adaptor contamination, low quality bases and undetermined bases.The transcriptome were de novo assembly. Results:A total of 54153182 raw reads were obtained from Illumina sequencing platform, and 53021436 clean reads were generated after filtering out the low quality reads. more...

Organism:

Quercus wutaishanica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26113

1 Sample

Download data: FASTA, TXT