70-mer oligonucleotide probes  (Operon Biotech)

Journal: BMC Plant Biology

Article Title: Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

doi: 10.1186/1471-2229-8-33

Figure Lengend Snippet: Validation of differential expression using MassArray and 70-mer platforms . The magnitude of differential expression between inbred lines based on the Affymetrix data was compared to the magnitude of differential expression detected using the MassArray platform and 70-mer microarray platform. The subset of the genes identified as differentially expressed on the Affymetrix platform (FDR < 0.05, and additional quality control filters; see Methods) was used for these analyses. The color coding of the data points indicates the inbred genotype comparison. (A) The same inbred RNA samples used for Affymetrix microarray analyses were mixed in a pairwise 1:1 ratio and subjected to MassArray relative allelic quantification [25]. The correlation between the MassArray proportions and the proportions calculated from the Affymetrix dataset (inbred 1 signal divided by the sum of the two inbred signals) are shown. Each spot represents the proportion of one allele per inbred-inbred comparison. The B73 and Mo17 sequence SNPs were used to design the assays, thus this comparison is most highly represented in this analysis. (B) Many genes that were determined to be differentially expressed in the Affymetrix dataset were also present on the 70-mer microarray platform. The correlation of the inbred expression fold-differences on the 70-mer oligonucleotide microarray and the Affymetrix microarray are shown. Each spot represents the fold-differences of one gene per inbred-inbred comparison. The 70-mer microarray data validated the directionality of the Affymetrix microarray patterns in 84–91% of the differentially expressed profiles (see main text).

Article Snippet: We began by comparing the d/a values for these 221 examples of AHP or BLP expression in the Affymetrix data to the d/a values for these genes in the 70-mer oligonucleotide microarray data [see Additional file ].

Techniques: Expressing, Microarray, Sequencing

Journal: BMC Plant Biology

Article Title: Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

doi: 10.1186/1471-2229-8-33

Figure Lengend Snippet: Distribution of d/a values for 70-mer array differentially expressed genes . Distributions of d/a (type I) ratios for differentially expressed genes based on the 70-mer oligonucleotide microarray data. (A) The d/a distributions for all differentially expressed genes. The distributions of the four hybrids are very similar to one another and peak at approximately zero, as was observed in Affymetrix microarray data. (B) The d/a distributions for the subset of differentially expressed genes that are also represented with features on the Affymetrix platform. The distributions are similar to those in (A). In both (A) and (B), the proportion of DE genes with d/a values above 3.0 or below -3.0 are all plotted as a single data point. The proportion of d/a values above 3.0 and below -3.0 for hybrid B84 × B73 plotted beyond the range of the displays and are not shown.

Article Snippet: We began by comparing the d/a values for these 221 examples of AHP or BLP expression in the Affymetrix data to the d/a values for these genes in the 70-mer oligonucleotide microarray data [see Additional file ].

Techniques: Microarray