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Omics score: 38

Gene expression in leaves of a Populus trichocarpa and Populus deltoides pseudo-backcross population

ABSTRACT: A microarray analysis of whole-genome gene expression in leaves was carried out 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. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus. Overall design: Data include one biological replicate of 183 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots 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)

INSTRUMENT(S): UF Nimblegen Populus trichocarpa Array

ORGANISM(S): Populus trichocarpa x Populus deltoides

SUBMITTER: Matias Kirst

PROVIDER: GSE20117 | GEO | 2010-02-02

SECONDARY ACCESSION(S): PRJNA124253

REPOSITORIES: GEO

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Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Project description:A microarray analysis of whole-genome gene expression in roots was carried out 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. Resultant data contributed to the analysis of the genetic architecture of gene expression in roots of Populus. Overall design: Data include one biological replicate of 163 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots 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)

2010-02-02 | GSE20118 | GEO

Gene expression in leaves of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Project description:A microarray analysis of whole-genome gene expression in leaves was carried out 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. Resultant data contributed to the analysis of the genetic architecture of gene expression in leaves of Populus. Data include one biological replicate of 183 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots 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)

2010-06-24 | E-GEOD-20117 | ArrayExpress

Gene expression in whole-roots of a Populus trichocarpa and Populus deltoides pseudo-backcross population

Project description:A microarray analysis of whole-genome gene expression in roots was carried out 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. Resultant data contributed to the analysis of the genetic architecture of gene expression in roots of Populus. Data include one biological replicate of 163 individuals segregating from a pseudo-backcross pedigree of (Populus trichocarpa X Populus deltoides) X Populus deltoides analyzed for gene expression (GE) in roots 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)

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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 Overall design: 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 | GSE12623 | GEO

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

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2008-09-06 | E-GEOD-12623 | ArrayExpress

Screen of oligonucleotides for microarray transcriptome analysis of Populus deltoides and P. trichocarpa

Project description:The purpose of this study was to evaluate a set of 6-7 long oligonucleotide probes developed based on the sequence of the Populus trichocarpa genome, that are optimal for gene expression analysis of P. deltoides and a hybrid of P. deltoides and P. trichocarpa. To evaluate these probes, multiple tissues (differentiating xyle, leaf and whole-root) of a pure P. deltoides and a hybrid (P. deltoides X P. trichocarpa) were transcript profiled for identification of one or more probes that are not biased towards one or the other genotype. Overall design: Three vegetative tissues (root, leaf and xylem) harvested from two biological replicates from each genotypes of Populus deltoides (genotype D124) and a Populus hybrid (P. deltoides X P. trichocarpa, genotype 52-225) were hybridized separately to microarrays in a single-dye experiment.

2008-09-10 | GSE12492 | GEO

Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor

Project description:The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor. Overall design: The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

2011-01-15 | GSE26416 | GEO

Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor

Project description:The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor. The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

2011-01-15 | E-GEOD-26416 | ArrayExpress

Ozone Exposure of Populus

Project description:This SuperSeries is composed of the following subset Series: GSE10873: Ozone exposure of tolerant and sensitive F2 genotypes of Populus GSE10874: Ozone exposure of Populus deltoides and Populus trichocarpa Keywords: SuperSeries Refer to individual Series

2009-04-01 | E-GEOD-10932 | ArrayExpress

Populus trichocarpa x Populus deltoides

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

| PRJNA113089 | ENA

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