arabidopsis ath1 affymetrix gene chip  (Thermo Fisher)

Journal: Genome Biology

Article Title: Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

doi: 10.1186/gb-2010-11-12-r123

Figure Lengend Snippet: High-resolution kinetics of transcriptome responses to NO 3 - treatment . (a) Levels of mRNA for nitrogen-responsive sentinel genes in Arabidopsis roots in response to NO 3 - treatment. Fourteen-day-old plants grown in the presence of ammonium succinate were treated with 1 mM KNO 3 or KCL (as a mock treatment). Plants were collected at 0 minutes (before treatment) and 3, 6, 9, 12, 15, 20, 25, 35, 45, and 60 minutes after treatment. Sentinel transcripts were measured in RNA from roots using RT-QPCR and normalized to two housekeeping genes (see Materials and methods). The insets show the Affymetrix MAS5 normalized signal for the sentinel genes on the 0- to 20-minute samples. The data represent the mean ± standard error of three and two biological replicates for QPCR and Affymetrix measurements, respectively. (b) Percentage of genes not detected as NO 3 - regulated in Wang et al . . (c) Overall behavior (relative expression) of 550 regulated genes (Log base 2(Signal KNO 3 /Signal KCl)) between 0 and 20 minutes. These data correspond to ATH1 measurement of the samples collected for the RT-PCR presented in (a) (grey shades; see also Materials and methods for further details).

Article Snippet: Labeled cRNA (8 μg) was hybridized to Arabidopsis ATH1 Affymetrix gene chip for 16 h at 45°C.

Techniques: Quantitative RT-PCR, Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: Genome Biology

Article Title: Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

doi: 10.1186/gb-2010-11-12-r123

Figure Lengend Snippet: Clustering analysis and QPCR reveals different patterns of expression in response to short-term NO 3 - treatment . (a) Cluster analysis of the relative expression of 550 regulated genes (Log base 2(Signal KNO 3 /Signal KCl)) between 0 and 20 minutes. These data correspond to ATH1 measurement of the samples collected for the RT-PCR shown in Figure 1 (see Materials and methods for further details). For clusters including genes with a significant over-representation of biological functions see Additional file . (b) Examples of three different gene behaviors (transitory, early, late responses) after NO 3 - provision.

Article Snippet: Labeled cRNA (8 μg) was hybridized to Arabidopsis ATH1 Affymetrix gene chip for 16 h at 45°C.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: Genome Biology

Article Title: Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

doi: 10.1186/gb-2010-11-12-r123

Figure Lengend Snippet: High-resolution kinetics of transcriptome responses to NO 3 - treatment . (a) Levels of mRNA for nitrogen-responsive sentinel genes in Arabidopsis roots in response to NO 3 - treatment. Fourteen-day-old plants grown in the presence of ammonium succinate were treated with 1 mM KNO 3 or KCL (as a mock treatment). Plants were collected at 0 minutes (before treatment) and 3, 6, 9, 12, 15, 20, 25, 35, 45, and 60 minutes after treatment. Sentinel transcripts were measured in RNA from roots using RT-QPCR and normalized to two housekeeping genes (see Materials and methods). The insets show the Affymetrix MAS5 normalized signal for the sentinel genes on the 0- to 20-minute samples. The data represent the mean ± standard error of three and two biological replicates for QPCR and Affymetrix measurements, respectively. (b) Percentage of genes not detected as NO 3 - regulated in Wang et al . . (c) Overall behavior (relative expression) of 550 regulated genes (Log base 2(Signal KNO 3 /Signal KCl)) between 0 and 20 minutes. These data correspond to ATH1 measurement of the samples collected for the RT-PCR presented in (a) (grey shades; see also Materials and methods for further details).

Article Snippet: The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips.

Techniques: Quantitative RT-PCR, Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: Genome Biology

Article Title: Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate

doi: 10.1186/gb-2010-11-12-r123

Figure Lengend Snippet: Clustering analysis and QPCR reveals different patterns of expression in response to short-term NO 3 - treatment . (a) Cluster analysis of the relative expression of 550 regulated genes (Log base 2(Signal KNO 3 /Signal KCl)) between 0 and 20 minutes. These data correspond to ATH1 measurement of the samples collected for the RT-PCR shown in Figure 1 (see Materials and methods for further details). For clusters including genes with a significant over-representation of biological functions see Additional file . (b) Examples of three different gene behaviors (transitory, early, late responses) after NO 3 - provision.

Article Snippet: The experimental approach has been to monitor genome-wide responses to nitrate at 3, 6, 9, 12, 15 and 20 minutes using Affymetrix ATH1 gene chips.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

Journal: Molecular Systems Biology

Article Title: Plant stem cell maintenance involves direct transcriptional repression of differentiation program

doi: 10.1038/msb.2013.8

Figure Lengend Snippet: System for assaying WUS-response genes at higher spatial resolution. ( A ) A schematic of Arabidopsis shoot apical meristem (SAM) stem cell niche showing stem cell domain/the central zone (CZ), the organizing center (OC)/niche and differentiating region/the peripheral zone (PZ). Transcriptional domains of WUS , CLV3 and WUS protein gradient are highlighted in different colors. Mutual feedback regulation between CLV3 and WUS is shown. ( B , C ) Three-dimensional reconstructed top views of ap1-1;cal1-1 SAMs carrying Dex-inducible form of WUS ( 35S:;WUS-GR ), labeled with stem cell marker- pCLV3::mGFP-ER (green) in plants treated with mock and Dex, respectively, are shown. Arrows point to outer limits of stem cell domain and expansion of stem cell domain upon Dex treatment. Scale bar in (C) represents 25 μm and it remains same for (B). ( D ) qRT–PCR analysis showing temporal dynamics of CLV3 activation upon WUS induction. Error bars represent standard deviation for two biological replicates.

Article Snippet: Therefore, SAMs were treated with 10 μM Dex solution for 4 h and RNA samples were hybridized to Arabidopsis ATH1 gene Chip (Affymetrix).

Techniques: Labeling, Marker, Quantitative RT-PCR, Activation Assay, Standard Deviation

Journal: Molecular Systems Biology

Article Title: Plant stem cell maintenance involves direct transcriptional repression of differentiation program

doi: 10.1038/msb.2013.8

Figure Lengend Snippet: TAAT elements are required for WUS binding and repression. ( A – G ) EMSAs showing recombinant WUS protein bound to radiolabeled oligonucleotides corresponding to KAN1 , KAN2 , AS2 and YAB3 regulatory regions and mutant oligonucleotides versions of conserved TAAT sequences. A black arrowhead indicates free probe and a dark gray arrowhead band shift for KAN1 , KAN2 , AS2 and YAB3 radiolabeled oligonucleotides, respectively. The sequences of WUS bound oligonucleotides and mutants are shown in ( H ). All TAAT elements are underlined and TAAT elements that are essential for WUS binding are shown in bold letters. ( I ) The TAAT promoter element is essential for WUS-dependent repression of KAN1 in Arabidopsis leaf mesophyll protoplasts. Transient transfection assay plots showing repression of LUCIFERASE (LUC) reporter when cloned downstream of a region containing WUS-binding element found in KAN1 promoter (KAN1 +950, +1150:35s::LUC) and a mutated version (TGGT) of KAN1 promoter. The constructs were tested for transactivation of LUC by cotransfection with or without WUS. The cotransfection of UBIQUITIN::GUS served as an internal control. Activity was expressed as a ratio of firefly LUC/GUS activity. Three biological replicates were used for each experiment and the error bars represent the standard deviation.

Article Snippet: Therefore, SAMs were treated with 10 μM Dex solution for 4 h and RNA samples were hybridized to Arabidopsis ATH1 gene Chip (Affymetrix).

Techniques: Binding Assay, Recombinant, Mutagenesis, Electrophoretic Mobility Shift Assay, Transient Transfection Assay, Luciferase, Clone Assay, Construct, Cotransfection, Activity Assay, Standard Deviation

Journal: PLoS ONE

Article Title: Transcriptome Analysis Reveals Genes Commonly Induced by Botrytis cinerea Infection, Cold, Drought and Oxidative Stresses in Arabidopsis

doi: 10.1371/journal.pone.0113718

Figure Lengend Snippet: Changes in expression of up- or down-regulated genes during B. cinerea infection and abiotic stress treatments in Arabidopsis plants.

Article Snippet: A full microarray-based analysis of an Arabidopsis whole-genome Affymetrix gene chip (ATH1), representing approximately 25,000 genes, was downloaded from the NASC repository .

Techniques: Expressing, Infection