Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE73146 | GEO | 2015/09/18
SECONDARY ACCESSION(S): PRJNA296068
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptomic analysis of gene expression during the differentiation of cell suspension cultures into tracheary elements using the biological system published by Pesquet et al., Current Biology (2010): tracheary element differentiation was triggered by externally supplying hormone-free habituated cell suspension cultures of Arabidopsis thaliana Col-0 with auxin, cytokinin and epibrassinolides; RNA samples extracted from 3 independent time-courses every 12h from 0h to 4 days were analyzed using ATH1 Arabidopsis Affymetrix micro-array Time-course design during tracheary element differentiation (3 independepent time-course were harvested from initiation 0h to 4 days every 12h) - total of 27 samples corresponding to the 3 replicates of 9 time point time-courses - gene expression was monitored along the time-course compared to 0h
2015-09-18 | E-GEOD-73146 | biostudies-arrayexpress
Project description:The growth of Arabidopsis cell cultures following their sub-culture into fresh media follows standard growth kinetics of a period of exponential increase associated with high rate of cell division, followed by a slowing of the rate of increase as cells approach stationary phase. For the analysis described here, MM2d cells were subcultured into fresh MSS-medium and samples were taken at day 1, day3, day 5 and day7. We have carried out transcriptional profiling analysis with the aim to follow growth stage specific gene expression during unperturbed growth using the near full genome ATH1 arrays (Menges et al., 2003). Journal Absract: (Plant Molecular Biology: 53, 2003) Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Analysis of gene expression profiles during normal culture growth, during synchronous cell cycle re-entry and during synchronous cell cycle progression provides a unique integrated view of gene expression responses in a higher-plant system. Particularly striking is that expression of over 14 000 genes belonging to all defined categories can be reliably detected, suggesting that integrated and comparative analysis of data sets derived from transcript profiling of cultures is a powerful approach to identify candidate components involved in a wide range of biological processes. Combinatorial analysis of independent cell cycle synchrony methods allows the identification of genes that are apparently cell-cycle-regulated but are most likely responding to the induction of synchrony. We thus present an integrated genome-wide view of the transcriptional profile of a plant suspension culture and identify a refined set of 1082 cell cycle regulated genes largely independent of synchrony method. Experimenter name = Jim Murray Experimenter phone = 44 1223 334166 Experimenter fax = 44 1223 334162 Experimenter department = J Murray Laboratory Experimenter address = University of Cambridge Experimenter address = Institute of Biotechnology Experimenter address = Tennis Court Road Experimenter address = Cambridge Experimenter zip/postal_code = CB2 1QT Experimenter country = United Kingdom Keywords: time_series_design
2007-01-08 | GSE5750 | GEO
Project description:Xylem consists of three types of cells: vessel cells, also referred to as tracheary elements (TEs), parenchyma cells, and fiber cells. TE differentiation includes two essential processes, programmed cell death (PCD) and secondary cell wall formation. These two processes are tightly coupled. However, little is known about the molecular mechanism of their gene regulation. Here, we show that VASCULAR-RELATED NAC-DOMAIN 6 (VND6), a master regulator of TEs, regulates these processes in a coordinated manner. We first identified specific genes downstream of VND6 by comparing them with those of SECONDARY WALL-ASSOCIATES NAC DOMAIN PROTEIN1 (SND1), a master regulator of xylem fiber cells, with transformed suspension culture cells in microarray experiments.
2010-10-28 | GSE20586 | GEO
Project description:Gene expression over the course of xylem tracheary element formation in cell suspension cultures of Arabidopsis thaliana
| PRJNA296068 | ENA
Project description:Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose. A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.
2014-05-16 | E-GEOD-57751 | biostudies-arrayexpress
Project description:The growth of Arabidopsis cell cultures following their sub-culture into fresh media follows standard growth kinetics of a period of exponential increase associated with high rate of cell division, followed by a slowing of the rate of increase as cells approach stationary phase. For the analysis described here, MM2d cells were subcultured into fresh MSS-medium and samples were taken at day 1, day3, day 5 and day7. We have carried out transcriptional profiling analysis with the aim to follow growth stage specific gene expression during unperturbed growth using the near full genome ATH1 arrays (Menges et al., 2003). Journal Absract:; (Plant Molecular Biology: 53, 2003); Plant cell suspension cultures are invaluable models for the study of cellular processes. Here we develop the recently described Arabidopsis suspension culture MM2d as a transcript profiling platform by means of Affymetrix ATH1 microarrays. Analysis of gene expression profiles during normal culture growth, during synchronous cell cycle re-entry and during synchronous cell cycle progression provides a unique integrated view of gene expression responses in a higher-plant system. Particularly striking is that expression of over 14 000 genes belonging to all defined categories can be reliably detected, suggesting that integrated and comparative analysis of data sets derived from transcript profiling of cultures is a powerful approach to identify candidate components involved in a wide range of biological processes. Combinatorial analysis of independent cell cycle synchrony methods allows the identification of genes that are apparently cell-cycle-regulated but are most likely responding to the induction of synchrony. We thus present an integrated genome-wide view of the transcriptional profile of a plant suspension culture and identify a refined set of 1082 cell cycle regulated genes largely independent of synchrony method. Experimenter name = Jim Murray; Experimenter phone = 44 1223 334166; Experimenter fax = 44 1223 334162; Experimenter department = J Murray Laboratory; Experimenter address = University of Cambridge; Experimenter address = Institute of Biotechnology; Experimenter address = Tennis Court Road; Experimenter address = Cambridge; Experimenter zip/postal_code = CB2 1QT; Experimenter country = United Kingdom Experiment Overall Design: 4 samples were used in this experiment
2008-06-14 | E-GEOD-5750 | biostudies-arrayexpress
Project description:The extracellular matrix (ECM)-regulated phenotypic plasticity is crucial for metastatic progression of triple negative breast cancer (TNBC). To investigate the effect of matrix cues on phenotypic plasticity, we embedded triple negative DU4475 cells from suspension culture into mechanically tunable fibrin gels or basement membrane extract (Matrigel). Cells in suspension culture and matrix cultures showed divergent gene expression profiles, with specific gene expression signatures depending on the biochemical composition and stiffness of the matrix.
2023-04-05 | GSE228939 | GEO
Project description:Analysis of effect of hindlimb suspension and reloading on C57Bl/6 mouse soleus muscle. Experimental groups examined: -Control mice, 14 days -Hindlimb suspension for 7 days -Hindlimb suspension for 7 days, and subsequent reloading for 1 day -Hindlimb suspension for 7 days, and subsequent reloading for 7 days Keywords: other
2004-09-30 | GSE1293 | GEO
Project description:Environmental bacteria suspension Raw sequence reads
| PRJNA705060 | ENA
Project description:Transcriptional profiling after inhibition of cellulose synthesis by thaxtomin A and isoxaben in Arabidopsis thaliana suspension cells Perturbations in the cellulose content of the plant cell wall lead to global modifications in cellular homeostasis, as seen in cellulose synthase mutants or after inhibiting cellulose synthesis. In particular, application of inhibitors of cellulose synthesis such as thaxtomin A (TA) and isoxaben (IXB) initiates a programmed cell death (PCD) in Arabidopsis thaliana suspension cells that is dependent on de novo gene transcription. To further understand how TA and IXB activate PCD, a whole genome microarray analysis was performed on mRNA isolated from Arabidopsis suspension cells exposed to TA and IXB. More than 75% of the genes upregulated by TA were also upregulated by IXB, including genes encoding cell wall-related and calcium-binding proteins, defence/stress-related transcription factors, signalling components and cell death-related proteins. Comparisons with published transcriptional analyses revealed an important subset of genes generally induced in response to various biotic and abiotic stress.
2009-08-27 | GSE17824 | GEO