Populus tremula x Populus alba
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ABSTRACT:
PROVIDER: PRJNA137607 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done. 4 arrays - poplar; normal vs rnai mutant comparaison
2011-09-29 | E-GEOD-27063 | biostudies-arrayexpress
Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done.
2011-09-30 | GSE27063 | GEO
Project description:affy_pop_2011_08 - poplar bent study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-- The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology) - 27 arrays - poplar; gene knock in (transgenic)
2013-08-01 | GSE44321 | GEO
Project description:affy_pop_2011_08 - poplar estradiol study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology)
2013-07-01 | GSE43533 | GEO
Project description:Plants transition through juvenile and adult phases of vegetative development in a process known as vegetative phase change (VPC). In poplars (genus Populus) the differences between these stages are subtle, making it difficult to determine when this transition occurs. Previous studies of VPC in poplars have relied on plants propagated in vitro, leaving the natural progression of this process unknown. We examined developmental morphology of seed-grown and in vitro derived Populus tremula × alba (clone 717-1B4), and compared the phenotype of these to transgenics with manipulated miR156 expression, the master regulator of VPC. In seed-grown plants, most traits changed from node-to-node during the first 3 months of development but remained constant after node 25. Many traits remained unchanged in clones over-expressing miR156, or were enhanced when miR156 was lowered, demonstrating their natural progression is regulated by the miR156/SPL pathway. The characteristic leaf fluttering of Populus is one of these miR156-regulated traits. Vegetative development in plants grown from culture mirrored that of seed-grown plants, allowing direct comparison between plants often used in research and those found in nature. These results provide a foundation for further research on the role of VPC in the ecology and evolution of this economically important genus.
| S-EPMC8353317 | biostudies-literature
Project description:affy_pop_2011_08 - poplar bent study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-- The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology) - 27 arrays - poplar; gene knock in (transgenic) 27 samples are wt; for this experiment only the bending comparaison are studied.
2013-08-01 | E-GEOD-44321 | biostudies-arrayexpress
Project description:affy_pop_2011_08 - poplar estradiol study - genes regulated by PtaZFP2 in absence of mechanical stress - genes regulated by PtaZFP2 after one bending.Species: Populus tremula x Populus alba-The laboratory previously established a poplar transgenic line overexpressing PtaZFP2 under the control of an estradiol-inducible promoter. - the experiment, conducted on 3-month-old hydroponically-grown poplars, consists in the comparison of WT poplars treated with estradiol and the PtaZFP2-overexpressing line treated with estradiol. We also compared unbent and bent PtaZFP2-overexpressing poplars. The applied strain is quantitatively controlled (Coutand & Moulia, 2000, JExpBot; coutand et al., 2009, Plant Physiology) 9 arrays - poplar; time course
2013-07-01 | E-GEOD-43533 | biostudies-arrayexpress
Project description:Poplar 84K (Populus alba x P. tremula var. glandulosa) is a fast-growing poplar hybrid. Originated in South Korea, this hybrid has been extensively cultivated in northern China. Due to the economic and ecological importance of this hybrid and high transformability, we now report the de novo sequencing and assembly of a male individual of poplar 84K using PacBio and Hi-C technologies. The final reference nuclear genome (747.5?Mb) has a contig N50 size of 1.99?Mb and a scaffold N50 size of 19.6?Mb. Complete chloroplast and mitochondrial genomes were also assembled from the sequencing data. Based on similarities to the genomes of P. alba var. pyramidalis and P. tremula, we were able to identify two subgenomes, representing 356?Mb from P. alba (subgenome A) and 354?Mb from P. tremula var. glandulosa (subgenome G). The phased assembly allowed us to detect the transcriptional bias between the two subgenomes, and we found that the subgenome from P. tremula displayed dominant expression in both 84K and another widely used hybrid, P. tremula x P. alba. This high-quality poplar 84K genome will be a valuable resource for poplar breeding and for molecular biology studies.
| S-EPMC6796506 | biostudies-literature
Project description:Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.
2022-10-04 | GSE190649 | GEO
Project description:To obtain genes expression in different parts of 84k poplar stems, transcriptome sequencing was performed using Illumina Novaseq 6000 second-generation sequencing platform from Shanghai BIOZERON Co. Ltd (www.biozeron.com). Selecte three stem segments of plants REPEAT 1, 2 and 3 with good and similar growth to use: 2nd-3rd internodes (poplar stem top: PST1, PST2, PST3); 9th-10th internodes (poplar stem middle: PSM1, PSM2, PSM3); 14th-15th internodes (poplar stem bottom: PSB1, PSB2, PSB3). [Or the three repeating organisms are also called poplar A, B, C. From top to bottom, the three parts of the stem are also called stem 1, 2, 3.]
2021-10-28 | GSE186743 | GEO