Transcription profiling of Arabidopsis seedlings under conditions of salt stress for 6, 24 and 48 hours
ABSTRACT: Hydroponic cultured Arabidopis thaliana(ecotype Col-0) seeldings(18 days after germination)were treated with 1/2 X MS supplemented with 150 mM NaCl for 6, 24 and 48h, with roots harvested and pooled for RNA extraction. Control roots (1/2 X MS only)were also harvested at the same time for each time-point. 3 independent biological replicates were prepared for each time-point. Altogether 18 hybridizations including dye flips were performed with Qiagen Operon V1.0.2 26k microarray. Microarray data were analyzed using TIGR TM4 suite.
BACKGROUND: Roots are an attractive system for genomic and post-genomic studies of NaCl responses, due to their primary importance to agriculture, and because of their relative structural and biochemical simplicity. Excellent genomic resources have been established for the study of Arabidopsis roots, however, a comprehensive microarray analysis of the root transcriptome following NaCl exposure is required to further understand plant responses to abiotic stress and facilitate future, systems-base ...[more]
Project description:Arabidopsis (wildtype and T-DNA insertion mutant bhlh92) was hydroponicaly cultured for 20 dand treated with 1/2 x MS supplemented with 150 mM NaCl for 6 h. RNA was extracted from roots of wildtype and bhlh92 mutants. Reverse transcription and microarray hybridization was performed to identify the differentially expressed between wildtype and bhlh92 mutants.
Project description:Arabidopsis thaliana, wild-type (Col-0) and a T-DNA insertion mutant of WRKY25 gene(SAIL_529_B11, designated as wrky25-1),were hydroponically cultured for 20 d and treated with 1/2 x MS supplemented with 150 mM NaCl for 6 h. Roots were harvested and RNA samples were prepared. QiagenOperon oligonucleotide microarray(v1.0.3) was used to identify differentially expressed genes in wrky25-1 mutant compared to wild-type under salt stress treatment. Microarray profilings were performed with three independent biological replicates prepared at separate time.
Project description:Arabidopsis thaliana, wild-type (Col-0) and a T-DNA insertion mutant of WRKY33 gene(SALK_006603, designated as wrky33-1),were hydroponically cultured for 20 d and treated by 150 mM NaCl for 6 h. Roots were harvested and a QiagenOperon oligonucleotide microarray(v1.0.3) was used to identify differentially expressed genes in wrky33-1 mutant compared to wild-type.
Project description:Brassica napus leaves(18 days old) were inoculated by Sclerotinia sclerotiorum with leaves harvested after 12, 24 and 48 h. Arabidopsis thaliana full-genome 70mer microarray representing at least 23,686 genes were used.
Project description:Competition is a major determinant of plant community structure consisting of both species-specific and general interactions, either of which may influence competitive competency and plant abundance and size. In certain cases, competitive competency could arise from altered gene expression and plant function when an individual is confronted with new competitors. We explored competition at the molecular level by hybridizing transcripts from Centaurea maculosa (spotted knapweed), one of North America's most invasive exotic plant species, to an Arabidopsis microarray chip. Centaurea was grown in competition with Festuca idahoensis (Idaho fescue), a native grass species that generally has weak competitive effects against Centaurea; Gaillardia aristata (Indian blanketflower), a native herbaceous species that tends to be a much stronger competitor against Centaurea; or alone (control). The expression of some genes was found to be relatively uninfluenced by the type of plant neighbor, whereas other patterns of gene expression appeared to be more neighbor specific. To our knowledge, these results are the first to identify genes in an invasive plant that are induced or repressed by plant neighbors and provide a new avenue of insight into the molecular aspects of plant competitive ability. Keywords: treated vs.untreated First file, Chip 508 (9-9-05) is preliminary hyb data to see if this cross species hybridization is possible using the OAR27K chip Experiment 1 (chip 508): The Arabidopsis OAR27K gene chip was hybridized with labeled cDNA probes produced from samples of Centaurea RNA at the W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University. The OAR27K gene chip consists of 70-mer oligos representing approximately 27,000 genes from Arabidopsis. Leaf and root samples were reverse-transcribed into cDNA and labeled with different fluorescent dyes (Cy3 and Cy5) using the Genisphere Array 900 kit (Cat No.W500180) (Genisphere, Hatfield PA). Labeled cDNAs were hybridized to the OAR27Kchip using the Advalytix ArrayBooster DNA Microarray Incubator (Advalytix, Boston MA). Approximately 10ug of each sample was used for hybridization.Experiment 2: Hybridization and labeling followed the procedure above, except the experimental control was Centaurea plants grown alone, and the test situations were Centaurea grown with Gaillardia or Festuca neighbors. In each experiment, RNA from Centaurea grown alone was used as the control (labeled with Cy3) and RNA from Centaurea grown with a neighbor was used as the test (labeled with Cy5). Two replicates were performed for each test situation.
Project description:Gene expression signatures encompassing dozens to hundreds of genes have been associated with many important parameters of cancer, but mechanisms of their control are largely unknown. Here we present a method based on genetic linkage that can prospectively identify functional regulators driving large-scale transcriptional signatures in cancer. Using this method we show that the wound response signature, a poor-prognosis expression pattern of 512 genes in breast cancer, is induced by coordinate amplifications of MYC and CSN5 (also known as JAB1 or COPS5). This information enabled experimental recapitulation, functional assessment and mechanistic elucidation of the wound signature in breast epithelial cells. A cell type comparison design experiment design type compares cells of different type for example different cell lines. Computed
Project description:Gene expression signatures encompassing dozens to hundreds of genes have been associated with many important parameters of cancer, but mechanisms of their control are largely unknown. Here we present a method based on genetic linkage that can prospectively identify functional regulators driving large-scale transcriptional signatures in cancer. Using this method we show that the wound response signature, a poor-prognosis expression pattern of 512 genes in breast cancer, is induced by coordinate amplifications of MYC and CSN5 (also known as JAB1 or COPS5). This information enabled experimental recapitulation, functional assessment and mechanistic elucidation of the wound signature in breast epithelial cells.
Project description:To mimic natural flooding conditions, we have adopted an “open system” treatment, in which only roots are subjected to hypoxia treatment. Using microarray analysis, we identified a number of AP2/ERF genes in Arabidopsis that are induced at different stages of hypoxia treatment. we performed microarray analysis to compare gene expression profiles of wild-type and AtERF73/HRE1-RNAi20 upon normaxic or hypoxic condition, in which AtERF73/HRE1 expression was severely knocked down. Arabidopsis Affymetrix GeneChip arrays were probed with RNAs isolated from roots of untreated plants (controls) and plants treated with hypoxia for 6 h.
Project description:Subolesin is an evolutionary conserved protein that was recently discovered in Ixodes scapularis as a tick protective antigen and has a role in tick blood digestion, reproduction and development. In other organisms, subolesin orthologs may be involved in the control of developmental processes. Because of the profound effect of subolesin knockdown in ticks and other organisms, we hypothesized that subolesin has a role in gene expression, thus affecting multiple cellular processes. The objective of this study was to provide support for the role of subolesin in gene expression. Keywords: time course Total RNA was prepared and pooled from subolesin dsRNA- and saline-injected ticks at 6 and 9 dpi (5 and 8 days of feeding).
Project description:Comparing gene expression in a Bellringer overexpressor vs wild-type Col-0. 3 biological sample replicates were used for microarray analyses.<br> <br> In order to control against dye bias and dye specific artifacts the replicate arrays had a "dye swop" design:<br> <br> Array 1: cy5 Col-0 a; cy5 BLR-OX_Van a<br> Array 2: cy5 BLR-OX_Van b; cy5 Col-0 b<br> Array 3: cy5 Col-0 c; cy5 BLR-OX_Van c