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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from two year old newly formed developing xylem and lignified xylem of Populus tomentosa

ABSTRACT: We take the two year old plant for sampling. Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa newly formed developing xylem and lignified xylem. We used microarrays to detail the global programme of gene expression in newly formed developing xylem and lignified xylem. Populus tomentosa newly formed developing xylem and lignified xylem were taken for RNA extraction and hybridization on Affymetrix microarrays. CB2009304-A and CB2009304-B from newly formed developing xylem, CB2009304-G and CB2009304-H from lignified xylem.

ORGANISM(S): Populus tomentosa

SUBMITTER: xiaohui yang

PROVIDER: E-GEOD-46946 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from two year old newly formed developing xylem and lignified xylem of Populus tomentosa

Project description:We take the two year old plant for sampling. Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa newly formed developing xylem and lignified xylem. We used microarrays to detail the global programme of gene expression in newly formed developing xylem and lignified xylem.

2013-05-16 | GSE46946 | GEO

Expression data from two year old shoot apex and mature xylem of Populus tomentosa

Project description:We take the two year old plant for sampling.Use the Affymetrix poplar gene chip to elucidate the gene functions and mechanisms in Populus tomentosa shoot apex and mature xylem. We used microarrays to detail the global programme of gene expression in shoot apex and mature xylem. Populus tomentosa shoot apex and mature xylem were taken for RNA extraction and hybridization on Affymetrix microarrays.CB2009304-C and CB2009304-D from shoot apex, CB2009304-G and CB2009304-H from mature xylem.

2013-04-23 | E-GEOD-46312 | biostudies-arrayexpress

Populus tomentosa

Project description:Expression data from two year old newly formed developing xylem and lignified xylem of Populus tomentosa

| PRJNA203122 | ENA

Expression data from leaf of (P. tomentosa x P. bolleana) x P. tomentosa under elevated CO2 concentrations

Project description:The atmosphere CO2 concentration keeps increasing every year. Use the Affymetrix poplar gene chip to confirm the expression changes in key genes in the triploid white poplar due to the influence of elevated CO2 concentrations. We used microarrays to detail the global programme of gene expression under normal and elevated CO2 concentrations. Gene expression of triploid white poplar ((P. tomentosa Ã? P. bolleanaï¼?Ã? P. tomentosa) leaves were investigated by using the Affymetrix poplar genome gene chip, after grown in controlled environment chambers under three different CO2 concentrations. Poplar leaves were subjected to normal CO2 concentrations (T0) and elevated CO2 concentrations (T1, 550 ppm and T2, 720 ppm) treatments three months.

2014-05-24 | E-GEOD-55216 | biostudies-arrayexpress

Expression data from two year old shoot apex and mature xylem of Populus tomentosa

2013-04-23 | GSE46312 | GEO

Expression data from OsEBS-transgenic rice B10201 and B10301 and control Guichao2

Project description:In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops.The identification of different yield related QTLs facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. In the present study, We cloned and characterized a large-panicle QTL, and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an average of 37.62% increase in total grain yield per plant. trait loci (QTLs) and are derived from variation inherent in crops. OsEBS-transgenic rice B10201 and B10301 and control Guichao2

2013-05-04 | E-GEOD-46616 | biostudies-arrayexpress

Transcriptome reorganization during wood maturation in Pinus radiata

Project description:Wood maturation produces two distinct wood tissues: juvenile wood (JW) and mature wood (LW), which are the major cause of wood qaulity variation within a tree. We investigate transcriptome reorganization during wood maturation process in radiata pine using a newly developed 18k cDNA microarrays. Developing xylem tissues from nine sampled trees at 5- and 13-year-old each were randomly divided into three groups with three trees each. Total RNA samples extracted from three trees within a group were pooled at equal amount before using for microarray experiments. Using this pooling strategy three biological replicates were formed for each microarray experiment. Dye swap was applied in each biological replicate. Comparisons between JW and MW in spring (EW) and autumn (LW) were arranged in two separate microarray experiments: juvenile earlywood (JE) vs. mature earlywood (ME), juvenile latewood (JL) vs. mature latewood (ML)

2011-06-01 | E-GEOD-20535 | biostudies-arrayexpress

Identification of candidate genes affecting juvenile wood density in Pinus radiata

Project description:Wood density is a foundamental quality trait for structural timber, bioenergy and pulp industries. We investigated genes differentially transcribed in radiate pine juvneile trees with distinct wood density using cDNA microarrays. Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

2012-08-02 | E-GEOD-32086 | biostudies-arrayexpress

Expression data from KOBU-induced Arabidopsis

Project description:Plant viruses induce various disease symptoms, but their underlying mechanisms are poorly understood. Kobu-sho is a disease in gentian that show gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Recently, we identified a novel unusual RNA virus, gentian Kobu-sho-associated virus (GKaV) from Kobu-sho-affected gentian. Here, we show that a gene fragment of GKaV, Kobu-sho-inducing factor (KOBU), induces gall formation accompanied with ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. We identify KOBU by screening using potato virus X vector in N. benthamiana, and confirm that transgenic gentian expressing KOBU causes tumorous symptom. Transgenic Arabidopsis thaliana expressing KOBU activates signaling pathways regulating xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within nucleus. Our findings provide novel insights into not only virus disease development but also vascular development in plant.

2018-04-01 | GSE107074 | GEO

RNA-seq transcriptome profiling in the Fagus sylvatica trunk

Project description:In a field study, trees from two sites in Lower Saxony, Germany, were compared. RNA-seq (performed on an Illumina HiSeq 2000) was conducted on RNA from developing xylem tissue from 4 different harvests throughout the growth season to analyze transcriptional changes related to variations in wood formation and development. A transcriptome contig database was created from the combined raw reads using ABySS. Mapping of reads from distinct samples to the contig database was performed using Bowtie.

2016-07-03 | E-MTAB-3615 | biostudies-arrayexpress

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