Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Soil below living and dead oak trees

ABSTRACT: Functional composition of deep soil microbial communities changes with oak mortality (raw sequence reads)

PROVIDER: PRJNA1191486 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Analysis of oak stem lesions in Acute Oak Decline using shotgun proteomics

Project description:Acute Oak Decline (AOD) is a decline-disease currently spreading in Britain, threatening oak trees. Here, we analyze and compare the proteomes of inner bark tissue sampled from oak stems of trees symptomatic with AOD and non-symptomatic trees.

2018-02-07 | PXD004991 | Pride

Transcriptomic analysis of Phanerochaete chrysosporium mycelium in presence of oak acetonic extractives

Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.

2014-08-13 | GSE54542 | GEO

Rhytidome- and cork- type barks of holm oak, cork oak and their hybrids highlight processes leading to cork formation

Project description: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. Cork is an outstanding model as it consists of a thick and very homogeneous periderm produced by a permanent mother-cell layer (phellogen). Conversely, holm oak contains a more heterogeneous bark including several thin periderms mixed with phloem, also known as a rhytidome. The inclusion of hybrid samples showing rhytidome-type and cork-type barks is valuable to approach cork development, allowing an accurate identification of candidate genes and processes. The present study underscores that biotic stress and cell death signalling are enhanced in rhytidome-type barks while lipid metabolism and cell cycle are enriched in cork-type barks. Based on the DEGs most expressed related to development, we highlight that cell division, cell expansion, and cell differentiation could account for the differences found between cork and rhytidome-type barks.

2024-06-12 | GSE227020 | GEO

Expression diversity of Phytophthora ramorum from canyon live oak

Project description:Expression diversity of P. ramorum isolates belonging to the NA1 clonal lineage growing on solid CV8 was examined. We found that phenotypes and transcriptomes change when isolates were passing through oak trees.

2014-10-24 | GSE62643 | GEO

PacBio Iso-Seq transcriptome for California Valley Oak, Quercus lobata (SW786)

Project description:Iso-Seq "full length" transcript sequences were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

2021-05-22 | GSE174827 | GEO

Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling

Project description: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. Studies in the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. We investigated the feasibility of such studies using heartwood samples core-drilled from the trunks of standing oak trees spanning the AD 1776-2014. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. We sequenced whole-genome and DNA methylome libraries for oak heartwood up to 100 and 50 years of age, respectively. However, only 56 genomic regions with sufficient coverage for quantitative methylation analysis were identified, suggesting that the high-throughput sequencing of DNA will be in principal feasible for wood formed <100 years ago is impeded by the reduction in library complexity caused by the bisulfite treatment used to generate the oak methylome.

2020-01-07 | GSE143201 | GEO

Whole genome bisulfite sequencing for bud, catkin and leaf of California Valley Oak, Quercus lobata (SW786)

Project description:WGBS sequencing of Valley Oak bud, catkin and leaf tissues

2021-05-22 | GSE174826 | GEO

Oak Bacteria

Project description:Identification of the oak microbiome

| PRJEB12457 | ENA

Illumina RNA-seq for bud, leaf and stem of California Valley Oak, Quercus lobata (SW786)

Project description:STAR aligned RNA-seq reads were used as one of many guides informing gene model annotation of the Valley Oak genome sequence.

2021-05-22 | GSE174828 | GEO

Effect of Oak extractives on the gene expression of Phanerochaete chrysosporium

Project description:Illumina HiSeq2500 technology was used to generate mRNA profiles from Phanerochaete chrysosporium treated with oak extractives for 1, 3 and 6h. 125bp pair-end reads were generated and aligned to the P.chrysosporium reference transcripts. (https://genome.jgi.doe.gov/Phchr2/Phchr2.home.html) using CLC Genomics Workbench 9.

2018-10-01 | GSE119735 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data