RNAseq of transfected protoplasts of Populus trichocarpa
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus trichocarpa
PROVIDER: GSE154167 | GEO | 2020/07/11
REPOSITORIES: GEO
Similar Datasets
Project description:We treated 6 month Populus trichocarpa by bending for 0, 3, and 7 days to see effects of bending treatment on wood formation at transcript level
2020-07-05 | GSE153793 | GEO
Project description:To identify genes that are drought-responsive we conducted drought (soil water depletion) experiments on 3-month-old *P*. *trichocarpa *clonal plants. The plants undergo five different stages based on the appearance of their shoots and leaves during the drought experiments. Stage I: The shoot and leaves are green, and the leaves are well-spread. Stage II: The leaves are droopy. Stage III: The shoot is droopy, and the leaves are partially dry. Stage IV: The leaves are brown and totally dry. Stage V: The shoot is brown. With fully irrigation, the soil water content is 74% and the xylem water content is 80.6%. Plants in Stage III (Day 5) are under a mild drought state. The soil and xylem water content in Stage III dropped to 33% and 75.3%, respectively. Stage IV (Day 6-10) is a severe drought state where the soil and xylem water content continued decreasing to 29% and 74.3%, respectively in Day 7. The stressed plants from Stage I-IV could all recover in 3 days after rehydration, but the plants in Stage V could not recover after rehydration.
2018-12-27 | GSE79401 | GEO
Project description:High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection. Developing xylem harvested at breast height from the north side of each tree stem from 17 genotypes with two biological replicates and from two additional genotypes without a second replicate previously identified as most extreme phenotypes in six wood traits was individually profiled for transcriptome analysis totaling 36 hybridizations to three NimbleGen 12-plex poplar arrays.
2013-02-26 | E-GEOD-44606 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Populus trichocarpa tissues (including leaves, xylem and mechanically-treated xylem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, xylem and mechanically-treated xylem of Populus trichocarpa, Nisqually-1 genotype. Total RNA was isolated using the Plant RNA Purification Reagent (Invitrogen), and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Vincent Chiang for providing the plant material as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.
2011-05-09 | E-GEOD-28984 | biostudies-arrayexpress
Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from Populus trichocarpa tissues (including leaves, xylem and mechanically-treated xylem). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study.
2011-05-10 | GSE28984 | GEO
Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course
2010-06-05 | GSE16459 | GEO
Project description:* In response to gravitational stresses, angiosperm trees form tension wood in the upper sides of branches and leaning stems in which cellulose content is higher, microfibrils are typically aligned closely with the fibre axis and the fibres often have a thick inner gelatinous cell wall layer (G-layer). * Gene expression was studied in Eucalyptus nitens branches oriented at 45° using microarrays containing 4 900 xylem cDNAs, and wood fibre characteristics revealed by X-ray diffraction, chemical and histochemical methods. * Xylem fibres in tension wood (upper branch) had a low microfibril angle, contained few fibres with G-layers and had higher cellulose and decreased Klason lignin compared to lower branch wood. Expression of two closely related fasciclin-like arabinogalactan proteins and a B-tubulin was inversely correlated with microfibril angle in upper and lower xylem from branches. * Structural and chemical modifications throughout the secondary cell walls of fibres sufficient to resist tension forces in branches can occur in the absence of G-layer enriched fibres and some important genes involved in responses to gravitational stress in eucalypt xylem are identified. Keywords: tissue comparison
2011-05-19 | GSE8816 | GEO
Project description:affy_orleans_circad - circad_pop1 - Global transcriptome analysis of tension wood in poplar over a 24h period. Young differentiating xylem was harvested on the tension wood side of 6 month-old poplar trees grown in greenhouse conditions. The samples were harvested at 6 hour intervals throughout the day. The bioinformatic analysis will permit the identification of genes expressed in tension wood and that cycle with a nycthemeral oscillation pattern. Keywords: time course 10 arrays - poplar
2010-06-16 | E-GEOD-16459 | biostudies-arrayexpress
Project description:Populus deltoides and Populus trichocarpa were exposed to either ambient air or an acute ozone exposure of 200 ppb for 9 hrs and ozone response was profiled for each genotype by hybridising control against ozone-exposed samples per genotype. Keywords: stress response, genotype comparrison, ozone exposure
2009-04-01 | GSE10874 | GEO
Project description:High-throughput approaches have been widely applied to elucidate the genetic underpinnings of industrially important wood properties. Each single wood trait was found to be highly polygenic in its nature. However, gene hierarchies need to be assessed with the most important gene variants controlling a specific trait within the complex network of interacting secondary cell wall characteristics that defines the overall wood phenotype. We tested the available genetic and genomic information in an integrative approach to effectively predict wood properties in Populus trichocarpa.Nine-yr-old natural P. trichocarpa trees including accessions with high contrasts in six traits related to wood chemistry and ultrastructure were profiled for gene expression on 49K Nimblegen array elements and for 28,831 polymorphic SNPs. Pre-selected transcripts and SNPs with high statistical dependency on the phenotypic trait were used in a Bayesian network learning procedure with stepwise K2 algorithm to infer phenotype-centric networks. Transcripts were pre-selected at much lower logBF threshold than SNPs and were not accommodated in the networks. Complexity of phenotype-centric networks with 100% predictive accuracy ranged from 7 (glucose) to 39 SNPs (alpha-cellulose). Pleiotropic gene actions were accommodated in genetic networks of correlated traits; such gene variants help to understand independent evolution of trait values, and they represent new tools to support the maximization of correlated response to selection.
2013-02-26 | GSE44606 | GEO