microarray-based gene expression analysis guide  (Agilent technologies)

Journal: Journal of Experimental Botany

Article Title: NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine

doi: 10.1093/jxb/erad507

Figure Lengend Snippet: NAC61 expression analysis. (A) NAC61 expression behavior in grapevine organs throughout development (bar plot) and compared in the heatmap (logarithmic value) with that of NAC60 and NAC33. The data were retrieved from the atlas transcriptomic dataset of cv. ‘Corvina’ ( Fasoli et al ., 2012 ). Each value represents the mean ±SD of three biological replicates. (B) Correlation between NAC61 expression level and sugar content in grape berries sampled from fruit set to maturity in cv. ‘Cabernet Sauvignon’ and cv. ‘Pinot noir’ ( Fasoli et al ., 2018 ). The black line represents the trend of the averaged values of the two varieties. The R 2 values shown correspond to the fitting of different polynomial regressions to each corresponding group of samples (orange for cv. ‘Cabernet Sauvignon’ samples, blue for cv. ‘Pinot noir’ samples, and black for the entire set of samples). (C) Correlation between NAC61 expression level and sugar content in grape berries sampled during post-harvest dehydration in six different varieties ( Zenoni et al ., 2016 ). (D) Correlation between NAC61 expression level and berry weight loss in cv. ‘Corvina’ berries sampled during traditional long and forced short post-harvest dehydration processes ( Zenoni et al ., 2020 ). Expression values were determined by microarray analysis and each value represents the mean ±SD from three biological replicates. (E) NAC61 GCNs based on berry, leaf, and tissue-independent (TI) datasets. Left, Venn diagram showing exclusive and shared genes based on the three datasets; right, three-dimensional plot of co-expressed genes in which NAC, WRKY, and ZIP family members already described as having involvement in berry ripening and/or stress responses are indicated.

Article Snippet: The cDNA synthesis, labelling, hybridization, and washing steps were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide ( https://www.agilent.com/cs/library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.9.pdf ).

Techniques: Expressing, Microarray

Journal: Frontiers in Plant Science

Article Title: A Grapevine TTG2-Like WRKY Transcription Factor Is Involved in Regulating Vacuolar Transport and Flavonoid Biosynthesis

doi: 10.3389/fpls.2016.01979

Figure Lengend Snippet: Expression analyses in petunia petals by qPCR. (A) Expression analysis of F3 ′ H and N21 in the ph3 mutant and in VvWRKY26 expressing lines as confirmation of the microarray results. (B) Expression analysis of structural genes related to vacuolar acidification (PhPH5 and PhPH1) and to anthocyanin synthesis (PhCHS-A and PhDFR-A) in the untransformed R27 and ph3 lines and VvWRKY26 expressing plants. In all analyses the data correspond to the mean ± SE of three biological replicates (corresponding to lines 1, 2, and 5; Supplementary Figure ) relative to an ACTIN housekeeping control and normalized against the ph3 mutant value. Abbreviations correspond to: PhF3 ′ H, FLAVONOID-3 ′ -MONOOXYGENASE; PhN21, NODULIN MTN21-LIKE PROTEIN; PhPH5, H + P 3 A -ATPASE; PhPH1, P 3 B -ATPASE; PhCHS-A, CHALCONE SYNTHASE A; PhDFR-A, DIHYDROFLAVONOL 4-REDUCTASE A .

Article Snippet: For microarray analysis on Sultana leaves transiently over-expressing VvWRKY26 , the cDNA synthesis, labeling, hybridization and washing reactions were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5).

Techniques: Expressing, Mutagenesis, Microarray

Journal: Molecular Plant Pathology

Article Title: Comparison of transcript profiles in different life stages of the nematode Globodera pallida under different host potato genotypes

doi: 10.1111/j.1364-3703.2012.00821.x

Figure Lengend Snippet: Reverse transcription‐polymerase chain reaction ( RT‐PCR ) validation. Gene expression from sedentary nematodes expressed as the fold change referenced to J 2 in the stages microarray experiment, and gene expression from sedentary nematodes in partially resistant line 11315 expressed as the fold change referenced to cv. D esirée in the genotypes microarray experiment

Article Snippet: All microarray hybridization and washing procedures were performed according to the Two‐Color Microarray‐Based Gene Expression Analysis Guide (version 5.7; Agilent Technologies).

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Microarray