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Transcription profiling of Populus stress response: nitrogen limitation, leaf wounding, and methyl jasmonate feeding of cell culture

ABSTRACT: This SuperSeries is composed of the following subset Series:; GSE16773: Gene expression response of Populus tremuloides cell suspension cultures to methyl jasmonate feeding; GSE16783: Wound-induced gene expression changes in Populus: 1 week; GSE16785: Wound-induced gene expression changes in Populus: 90 hours; GSE14893: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200; GSE14515: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979 Experiment Overall Design: Refer to individual Series

ORGANISM(S): Populus tremuloides

SUBMITTER: Chung-Jui Tsai

PROVIDER: E-GEOD-16786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of Populus leaves under nitrogen limitation

Project description:This SuperSeries is composed of the following subset Series:; GSE14515: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979; GSE14893: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200 Experiment Overall Design: Refer to individual Series

2009-03-01 | E-GEOD-14894 | biostudies-arrayexpress

Transcription profiling of Populus leaves under nitrogen limitation: clone 3200

Project description:Gene expression response of Populus plants subjected to hydroponic nitrogen manipulation was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus fremontii x angustifolia genotypes were grown hydroponically with either 5 mM (N+) or 0.125 mM (N-) nitrogen. Young leaves at Leaf Plastchron Index (LPI) 2 were sampled 4 weeks after the start of low N feeding. Mature leaves at Leaf Plastchron Index (LPI) 5 were sampled 4 or 8 weeks after the start of low N feeding. Two biological replicates were obtained for each condition.

2009-03-01 | E-GEOD-14893 | biostudies-arrayexpress

Transcription profiling of Populus leaves under nitrogen limitation

Project description:Gene expression response of Populus plants subjected to hydroponic nitrogen manipulation was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus fremontii x angustifolia genotypes were grown hydroponically with either 5 mM (N+) or 0.125 mM (N-) nitrogen. Young and mature leaves at Leaf Plastchron Index (LPI) 2 and 5, respectively, were sampled 4 weeks after the start of low N feeding. Two biological replicates were obtained for each condition.

2009-02-08 | E-GEOD-14515 | biostudies-arrayexpress

Transcription profiling of Populus to investigate wound-induced gene expression changes: 90 hours; clone RM5

Project description:Gene expression response of Populus plants subjected to leaf wounding was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus fremontii x angustifolia genotypes were grown hydroponically.Â Wounding treatment was applied by pinching leaves at Leaf Plastchron Index (LPI) 8-12 with pliers at a rate of 10 1-inch wounds per leaf.Â Root tips (terminal 1 cm) and mature leaves (LPI 5) were sampled 90 hours after the treatment. Two biological replicates were obtained for each condition.

2009-12-14 | E-GEOD-16785 | biostudies-arrayexpress

Transcription profiling of Populus wound induced gene expression changes 1 week; clone RM5

Project description:Gene expression response of Populus plants subjected to leaf wounding was analyzed using the Affymetrix poplar genome microarrays. Experiment Overall Design: Populus fremontii x angustifolia genotypes were grown hydroponically.Â Wounding treatment was applied by pinching leaves at Leaf Plastchron Index (LPI) 8-12 with pliers at a rate of 10 1-inch wounds per leaf.Â Young (LPI 0 and LPI 1) and mature leaves (LPI 5) were sampled 1 week after the treatment. Two biological replicates were obtained for each condition.

2009-12-05 | E-GEOD-16783 | biostudies-arrayexpress

Gene expression and intragenic polymorphism in a Populus trichocarpa and Populus deltoides pseudo-backcross pedigree

Project description:A microarray analysis of whole-genome gene expression and single feature polymorphism in a (Populus trichocarpa X Populus deltoides) X Populus deltoides pseudo-backcross pedigree. Genetic variation in gene expression was quantified for 55,793 predicted gene models based on a single probe per gene. Concurrently, sequence-level polymorphism was analyzed based on dedicated probes identified in a pilot study comprised of the two parent genotypes (GPL7169). Resultant data contributed to a high density genetic map and to analysis of the genetic architecture of gene expression in Populus. Keywords: Genetic analysis of gene expression and polymorphism, eQTL Data include one biological replicate of 178 segregating pseudobackcross progeny analyzed for gene expression (GE) using one probe per gene for 55793 independent gene models (probes E_POPLARSxxxxxPxxxxx) and single feature sequence polymorphism (SFP) using one probe per gene for 12084 independent gene models (probes G_POPLARSxxxxxPxxxxx). GE and SFP probes were selected from 6-7 probes per gene previously tested in a pilot study of the two parent trees of the cross (Populus deltoides X Populus trichocarpa).

2008-09-06 | E-GEOD-12623 | biostudies-arrayexpress

Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

Project description:Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6. mRNA profiles from Populus trichocarpa roots colonized by Laccaria bicolor for two, four and 12 weeks as well as from control roots and free-living mycelium were generated by using one lane of 37 bp Illumina GAIIx sequencing per sample.

2014-02-08 | E-GEOD-54789 | biostudies-arrayexpress

Transcription profiling of Populus x canescens and P. euphratica

Project description:Comparison of transcriptional states of Populus x canescens and P. euphratica under control conditions

2009-10-27 | E-MEXP-1928 | biostudies-arrayexpress

Transcriptional profiling of Populus leaves with altered SA levels

Project description:Salicylic acid (SA) has long been implicated in plant responses to oxidative stress. A direct assessment of SA effects in planta has been difficult, as SA-overproducing Arabidopsis mutants are compromised in growth or other developmental processes. We now report that transgenic Populus expressing a bacterial bifunctional SA synthase accumulated two to three orders of magnitude more total SA than wild type without affecting growth. Microarray experiments were performed to gauge the transcriptional responses of young source leaves to SA manipulation and/or heat stress. Differentially expressed genes due to SA perturbation or temperature treatment were identified. Co-expression network analysis was performed to identify key driver genes in SA-modulated response. Wild-type and transgenic Populus expressing cytosolic Irp9 (Irp9 line I6), plastidic Irp9 (FD-Irp9 lines F10 and F52) or NahG (NahG line N31) genes were maintained in two identical growth chambers at normal (NT, 27Â°C/17Â°C, day/night) or high (HT, 35Â°C/25Â°C) temperatures. Young source leaves at leaf plastochron index (LPI) 5 were sampled one week after the start of heat stress. Two biological replicates were used.

2013-08-01 | E-GEOD-42511 | biostudies-arrayexpress

Proteomic Analysis Reveals the Association between the Path-ways of Glutathione and α-Linolenic Acid Metabolism and Lanthanum Accumulation in Tea Plants

Project description:Tieguanyin (TGY) and Shuixian (SX) cultivars of Camellia sinensis were selected to explore the mechanism underlying the accumulation of the rare earth element lanthanum through proteomics. Roots and fresh leaves of TGY and SX with low- and high-accumulation potential for lanthanum, respectively, were studied; 845 differentially expressed proteins (DEPs) were identified. Gene ontology analysis showed that the DEPs are involved in redox processes and related to molecular functions, such as defense and oxidative stress reactions, catalytic activity, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis showed that DEPs were associated with glutathione (GSH) and α-linolenic acid metabolism, plant pathogen interaction, and oxidative phosphorylation. Thirty-seven proteins in the GSH metabolism pathway showed significant differences, of which 18 GSH S-transferases show differential expression patterns in the root system.The expression multiples of GST (TEA004130.1) and GST (TEA032216.1) in T1L and T0L were 6.84 and 4.06, respectively, which were significantly higher than those in S1L and S0L. The lanthanum-induced activation of the GSH-related antioxidant defense system may cause the difference in TGY and SX. The LOX2.1 (TEA011765.1) and LOX2.1 (TEA011776.1 expression ratios) in the α-linolenic acid metabolic pathway were 2.44 and 6.43 in T1R and T0R, respectively, which were significantly higher than those in S1R snd S0R. The other differential proteins were also sig-nificantly upregulated in TGY leaves.The synthesis of specific substances induces lantha-num-associated defense responses in TGY, which is of great significance for the stability of its yield.

2023-03-11 | PXD039195 | Pride

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