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Analysis of Affymetrix Probe Set Distribution for Soybean cDNA and gDNA Sequence Specificity

This study presents the distribution of Affymetrix probe sets based on their specificity for predicted soybean cDNA and gDNA sequences. We summarize the quantifiable genes corresponding to various probe sets, highlighting the number of probes targeting soybean rRNA and their match against gDNA and cDNA. The analysis includes sets that match multiple cDNAs, those that uniquely match a single cDNA, and probes that align with intronic regions, providing insight into gene expression quantification in soybean genomics.

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Analysis of Affymetrix Probe Set Distribution for Soybean cDNA and gDNA Sequence Specificity

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  1. Figure S1. Affymetrix probe set distribution according to specificity for soybean predicted cDNA and gDNA sequences. The numbers of genes quantifiable by the probe sets are indicated in parentheses. 48 probes against soybean rRNA Probe sets matching against soybean gDNA but not against predicted cDNA 1098 402 514 648 (604) 916 3557 (10915) Match against more than 2 cDNA Match against 2 cDNA exactly Match against 1 cDNA only Match against intron of one gene only Match against intron of one gene and against gDNA where no genes are predicted 13949 (11426) Match against intron of more than 2 genes 16509 (22568) Match against gDNA where no genes are predicted Do not match against soybean sequences Probe sets matching against predicted soybean cDNA sequences

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