CO1 and CO2 network analysis in poplar
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus tremula x Populus alba
SUBMITTER: Joshua Adams
PROVIDER: E-GEOD-28706 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We conducted microarray experiments by comparing constitutive constructs with appropriate controls, followed by the identification of downstream targets of Pro35S:CO1 Four samples of mature leaf tissues were collected from four independent lines of 35S:CO1 and pBI101. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-28689 | biostudies-arrayexpress
Project description:We conducted microarray experiments by comparing constitutive constructs with appropriate controls, followed by the identification of downstream targets of Pro35S:CO2. Four samples of mature leaf tissues were collected from four independent lines of 35S:CO2 and pBI101. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-28693 | biostudies-arrayexpress
Project description:We conducted microarray experiments by comparing constitutive and inducible Flowering Locus T1 (FT1) and FT2 constructs with appropriate controls, followed by the identification of common targets of Pro35S:FT1 and ProHSP:FT1 or Pro35S:FT2 and ProHSP:FT2. Independent samples of leaf tissues were collected from 1- to 2-year-old plants. Each replication represents an individual plant from one of the treatment lines. RNA was extracted from tissues and hybridized on the Affymetrix GeneChip Poplar Genome Array.
2011-05-23 | E-GEOD-24609 | biostudies-arrayexpress
Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral buds through the course of the year allowing for identification of changing developmental signals. We used RNA samples from floral buds, with bud scale removed, in the upper crown of a sexually mature Populus deltoides tree 2 hours after sunrise. Three independent samples of floral bud tissues with bud scales removes were collected from the upper crown of a single sexually mature male tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-29335 | biostudies-arrayexpress
Project description:We conducted micro-array analysis to quantify the global transcriptome variations in floral organs of a male and female tree allowing for identification of sex-linked transcripts. We used RNA samples from male floral buds in August and female floral buds in September. Bud scale were removed. While the sampling time differed, the developmental stage of the floral organs was similar between the male and female. Five independent samples of floral bud tissues with bud scales removes were collected from the upper crown of a sexually mature male tree and female tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array.
2011-12-29 | E-GEOD-29336 | biostudies-arrayexpress
Project description:We conducted micro-array analysis to quantify the global transcriptome variations in leaves through the course of the year allowing for identification of changing developmental signals. We used RNA samples from pre-formed and mature leaves in the upper crown of a sexually mature Populus deltoides tree 2 hours after sunrise. Three independent samples of leaf/pre-formed leaf tissues were collected from the upper crown of a single sexually mature tree. RNA was extracted from tissues and hybridized on Affymetrix Genechip Poplar Genome Array. Tissues represented two batches (batch 1 from 2005 and batch 2 from 2006). Therefore, March samples were used to normalize the other month samples within the same batch.
2011-05-23 | E-GEOD-24349 | biostudies-arrayexpress
Project description:Regeneration of transgenic cells remains a major obstacle to research and commercial deployment of transgenic plants for most species. Our aims are to improve knowledge of gene regulatory circuits important to meristem organization, and to identify regulatory genes that might be useful for improving the efficiency of regeneration during transformation. We analyzed gene expression during poplar regeneration using an Affymetrix GeneChip® array representing over 56,000 poplar transcripts. Experiment Overall Design: We focused on callus induction and shoot formation, thus sample RNAs were collected from tissues: prior to callus induction, 3 days and 15 days after callus induction, and 3 days and 8 days after the start of shoot induction. Experiment Overall Design: Two biological replicates were used for each of the five time points.
2009-12-04 | E-GEOD-12152 | biostudies-arrayexpress
Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.
2013-07-17 | E-GEOD-43162 | biostudies-arrayexpress
Project description:Poplar (Populus trichocarpa, clone Nisqually-1) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity. Diurnal (driven) conditions included 12L:12D light cycles and 25C/12C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (25C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (25C) and a low night temperature (12C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (25C, day; 12C, night). Light intensity and relative humidity were 700 micromol m-2s-2 and 50%, respectively. Three-month-old poplar plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual poplar plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.
2010-01-09 | E-MEXP-2509 | biostudies-arrayexpress
Project description:Lignocellulosic feedstock (i.e., wood) is gaining popularity as a source of fermentable sugars for liquid fuel production. To improve the quantity and quality of woody biomass, the developing xylem (DX) cell-specific genetic modification is desired. Bioinformatic analyses followed by the validation of cell type-specific transcriptomes led to the identification of 37 transcripts specifically expressed in DX. After further confirmation of DX-specific expression, we selected four genes (DX5, DX8, DX11 and DX15) to demonstrate the feasibility of our strategy. The promoter regions of selected DX genes were isolated and produced stable transformants of poplar by using transcriptional promoter:?-glucuronidase (GUS) fusion constructs. The GUS expression patterns of DX5 and ANAC073 (orthologous gene of Arabidopsis) revealed that these promoters were active in xylem cells in poplar at early seedling growth, and showed strongest expression in the developing xylem cells in the wood formation/development at later growth stages of poplar. DX specific and strong expression patterns of all the other DX promoters (DX8, DX11 and DX15) tested suggests that these promoters may be useful to control transgene expression in the DX cells of woody plants with the aim of the feedstock improvement. In order to identify specifically and strongly expressed genes from DX cells of woody plant, we generated the tissue/cell type-specific transcriptomes from poplar stem by using whole genome GeneChip technology (Affymetrix).
2012-07-06 | E-GEOD-30507 | biostudies-arrayexpress