Quantification

Another important issue is whether GeoChip can provide quantitative information. We have demonstrated that linear relationships were observed between target DNA or RNA concentrations and hybridization signal intensity using pure culture, mixed culture, and environmental samples without amplification (Rhee et al., 2004; Wu et al., 2001; Wu et al., 2006). With the WCGA approach, robust quantitative detection was observed by significant linear relationships between signal intensity and initial DNA concentrations or cell numbers (Wu et al. 2006) (Figure 3). These studies demonstrate that GeoChip can be used to quantitatively analyze environmental samples.

(A) Fluorescence images showing the detection sensitivity of pure genomic DNA in the presence of background DNA. More than 50 ng DNA is needed. (B) Fluorescence images showing RNA detection sensitivities with cells. More than 107 cells are needed. (C) Improved amplification sensitivity with modified reaction buffer (Lanes A1 and A2) and an unmodified commercially available buffer (Lanes B1 and B2) with 100 fg (lanes A1 and B1) and 10 fg (Lanes A2 and B2, 2 cells) of template DNA and a control without DNA (Lane, CK). (D) Comparison of DNA yields with modified and unmodified reaction buffer. The error bars are based on three replicate