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arabidopsis ath1 affymetrix gene chip  (Thermo Fisher)


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    Thermo Fisher arabidopsis ath1 affymetrix gene chip
    High-resolution kinetics of transcriptome responses to NO 3 - treatment . (a) Levels of mRNA for nitrogen-responsive sentinel genes in <t>Arabidopsis</t> 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 <t>ATH1</t> measurement of the samples collected for the RT-PCR presented in (a) (grey shades; see also Materials and methods for further details).
    Arabidopsis Ath1 Affymetrix Gene Chip, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate"

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

    Journal: Genome Biology

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

    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).
    Figure Legend 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).

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

    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.
    Figure Legend 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.

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction

    Related Articles

    cDNA Synthesis:

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Article Title: A Non-Canonical Function of Arabidopsis ERECTA Proteins in Gibberellin Signaling
    Article Snippet: .. Targets were prepared with a cDNA synthesis kit followed by biotin labeling with the IVT labeling kit (GeneChip 39IVT Express; Affymetrix) and hybridized to the ATH1 gene chip for 16h as recommended by the supplier. ..

    Control:

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Article Title: Specificity versus redundancy in the RAP2.4 transcription factor family of Arabidopsis thaliana : transcriptional regulation of genes for chloroplast peroxidases
    Article Snippet: .. Fig. 1 Regulation of RAP2.4 expression in Arabidopsis wildtype plants. a Comparison of the transcript abundance regulation of the seven on the Affimetrix ATH1 gene chip represented RAP2.4 transcription factor genes during development on the Genevestigator platform. b Relative transcript abundance for all eight RAP2.4 transcription factor genes 1 week at 10 °C higher and lower temperature and after 2 h at elevated light intensity relative to the transcript level of plants kept at control conditions as obtained by qRT-PCR. ..

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Gene Expression:

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Article Title: Summarizing and exploring data of a decade of cytokinin-related transcriptomics
    Article Snippet: .. Four data sources were used for the comparative analysis: (1) The meta-analysis of CATMA microarray results presented in this study; (2) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip focusing on studies with a similar experimental layout (Brenner et al., ); (3) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip based on a more broadly selected dataset (Bhargava et al., ); and (4) a global gene expression analysis in response to cytokinin using RNA sequencing (Bhargava et al., ). ..

    Article Title: Regulation of zinc deficiency and tolerance in plants
    Article Snippet: .. Targets were prepared with the one-cycle cDNA synthesis kit followed by biotin-labelling with the IVT labelling kit (GeneChip One-cycle target labelling and control reagents, Affymetrix, High Wycombe, U.K.) and hybridized to ATH1 gene chip for 16 h as recommended by the supplier (Gene expression analysis manual, Affymetrix). ..

    Microarray:

    Article Title: Summarizing and exploring data of a decade of cytokinin-related transcriptomics
    Article Snippet: .. Four data sources were used for the comparative analysis: (1) The meta-analysis of CATMA microarray results presented in this study; (2) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip focusing on studies with a similar experimental layout (Brenner et al., ); (3) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip based on a more broadly selected dataset (Bhargava et al., ); and (4) a global gene expression analysis in response to cytokinin using RNA sequencing (Bhargava et al., ). ..

    Article Title: AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes
    Article Snippet: DNA methylation is an important epigenetic modification that governs transcriptional regulation.. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins.. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility.

    Article Title: Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana
    Article Snippet: .. Since the microarray analysis of the TIBA-treated plants was performed with the Affimetrix ATH1 gene chip, the list contains 301 and not 321 genes. ..

    RNA Sequencing:

    Article Title: Summarizing and exploring data of a decade of cytokinin-related transcriptomics
    Article Snippet: .. Four data sources were used for the comparative analysis: (1) The meta-analysis of CATMA microarray results presented in this study; (2) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip focusing on studies with a similar experimental layout (Brenner et al., ); (3) a meta-analysis of publicly available datasets performed with the Affymetrix ATH1 gene chip based on a more broadly selected dataset (Bhargava et al., ); and (4) a global gene expression analysis in response to cytokinin using RNA sequencing (Bhargava et al., ). ..

    Mutagenesis:

    Article Title: AtMBD4: A methylated DNA binding protein negatively regulates a subset of phosphate starvation genes
    Article Snippet: DNA methylation is an important epigenetic modification that governs transcriptional regulation.. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins.. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility.

    Expressing:

    Article Title: Specificity versus redundancy in the RAP2.4 transcription factor family of Arabidopsis thaliana : transcriptional regulation of genes for chloroplast peroxidases
    Article Snippet: .. Fig. 1 Regulation of RAP2.4 expression in Arabidopsis wildtype plants. a Comparison of the transcript abundance regulation of the seven on the Affimetrix ATH1 gene chip represented RAP2.4 transcription factor genes during development on the Genevestigator platform. b Relative transcript abundance for all eight RAP2.4 transcription factor genes 1 week at 10 °C higher and lower temperature and after 2 h at elevated light intensity relative to the transcript level of plants kept at control conditions as obtained by qRT-PCR. ..

    Comparison:

    Article Title: Specificity versus redundancy in the RAP2.4 transcription factor family of Arabidopsis thaliana : transcriptional regulation of genes for chloroplast peroxidases
    Article Snippet: .. Fig. 1 Regulation of RAP2.4 expression in Arabidopsis wildtype plants. a Comparison of the transcript abundance regulation of the seven on the Affimetrix ATH1 gene chip represented RAP2.4 transcription factor genes during development on the Genevestigator platform. b Relative transcript abundance for all eight RAP2.4 transcription factor genes 1 week at 10 °C higher and lower temperature and after 2 h at elevated light intensity relative to the transcript level of plants kept at control conditions as obtained by qRT-PCR. ..

    Labeling:

    Article Title: A Non-Canonical Function of Arabidopsis ERECTA Proteins in Gibberellin Signaling
    Article Snippet: .. Targets were prepared with a cDNA synthesis kit followed by biotin labeling with the IVT labeling kit (GeneChip 39IVT Express; Affymetrix) and hybridized to the ATH1 gene chip for 16h as recommended by the supplier. ..



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    Image Search Results


    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).

    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

    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.

    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

    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).

    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

    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.

    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

    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.

    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

    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.

    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

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

    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