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Figure 1 | BMC Genomics

Figure 1

From: Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency

Figure 1

A positive relationship between cDNA pool size and the number of fragments per PCR. Linear regressions of average fragment numbers produced during in silico selective cDNA-AFLP PCRs against the absolute cDNA pool size in bp. Symbols indicate the average fragment numbers produced per enzyme combination and species for selective amplifications using 2 × 2 (diamonds), 2 × 3 (crosses) and 3 × 3 (pluses) selective base pairs, respectively. Duplicate species have been removed from this analysis. The numbers of selective base pairs used for each primer in the selective PCR are indicated, and regression lines have been added for each of the three amplification types. The correlation coefficient for each of the three datasets is 0.74. The production of fewer than 20 fragments per PCR minimizes the possibility of collisions [8], while up to 100 fragments per reaction are often desired when performing AFLP on genomic DNA [3]. A maximum of 450 fragments can be separated in the typical size range of AFLP screens (50-500 bp). Vertical reference lines indicate the total cDNA pool size range expected in a typical tissue expressing between 7500 and 15000 different cDNAs [24] assuming an average cDNA length of 1346 bp [12].

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