Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

ORGANISM(S): Quercus lobata

PROVIDER: GSE174827 | GEO | 2021/05/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

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

| PRJNA731858 | ENA

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

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

| PRJNA731859 | ENA

Foraging patterns of acorn woodpeckers (Melanerpes formicivorus) on valley oak (Quercus lobata Nee) in two California oak savanna-woodlands.

Project description: Not available

| S-EPMC3074073 | biostudies-literature

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

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

| PRJNA731857 | ENA

PacBio Iso-Seq transcriptome sequencing data of multiplexed maize cDNA

Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.

2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress

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

The Holm oak (Quercus ilex) proteome as defined by shotgun MS (nLC-MS/MS, Orbitrap) approach

Project description:Holm oak (Quercus ilex) is the most important and representative specie of the Mediterranean forest and of the Spanish agrosilvo-pastoral ecosystem “Dehesa”. Despite its environmental and economic interest, Holm oak is still an orphan species whose biology is very little known, especially at the molecular level. In this research, we have performed a shotgun proteomic approach (nLC-MSMS, Orbitrap) to analyze the Holm oak proteome, using, as starting material, a pool generated by mixing equal amounts of homogenized tissue, including embryo, cotyledons (from mature acorns), and leaves and roots (from 6-month old plantlets grown in a greenhouse under environmental conditions). The proteome generated will be the bases of further studies on population variability, growth, development and responses to stresses in this species.

2018-01-16 | PXD008001 | Pride

Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus).

Project description: Not available

| S-EPMC6167808 | biostudies-literature