Data on DNA gel sample load, gel electrophoresis, PCR and cost analysis

The data presented in this article provide supporting information to the related research article “Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples” (Kuhn et al., 2017) [1]. In that article, we compared the suitability of ten selected DNA extraction methods based on DNA quality, purity, quantity and applicability to universal PCR. Here we provide the data on the specific DNA gel sample load, all unreported gel images of crude DNA and PCR results, and the complete cost analysis for all tested extraction procedures and in addition two commercial DNA extraction kits for soil and water.


a b s t r a c t
The data presented in this article provide supporting information to the related research article "Comparison of ten different DNA extraction procedures with respect to their suitability for environmental samples" (Kuhn et al., 2017) [1]. In that article, we compared the suitability of ten selected DNA extraction methods based on DNA quality, purity, quantity and applicability to universal PCR. Here we provide the data on the specific DNA gel sample load, all unreported gel images of crude DNA and PCR results, and the complete cost analysis for all tested extraction procedures and in addition two commercial DNA extraction kits for soil and water.
& 2017 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).  Table 1 presents the DNA sample load (in µL) necessary to visualize the crude DNA on the agarose gels. Different DNA loads were used in order to achieve comparable DNA concentrations ranging between 250 and 300 ng on the gel. Higher DNA loads were necessary for visualization on the agarose gels, especially for the crude DNA extracts from the Havel River sediment (procedure A, D, F, G, and H).

Specifications
The visual DNA quality control of crude DNA extracts and PCR of procedures B, C, D, E, H, I and J is presented in Figs. 1-4. The results for crude DNA extracts and PCR amplification of procedure B and C (method according to [2]) were almost similar. In both cases, intensive fragmentation was found for crude DNA extracts of the activated sludge and no distinct genomic DNA band was visible (Fig. 1, D1 & E1). The crude DNA of the sediment and anaerobic digestion sludge indicated a good quality with lower content of impurities, while the quality of the crude DNA for the nitrifying sludge was lower. A higher content of impurities was visible on both gel images. Positive PCR amplification was only feasible for the anaerobic digestion sludge and showed a very good quality of the amplicon (Fig. 1, D2 & E2).
The results for the crude DNA extracts of procedure D and E (method according to [3,4]) were also almost similar (Fig. 2, F1 & G1). For procedure D, no distinct genomic DNA band was visible on the agarose gel but instead, fragmentation and higher content of undefined impurities (Fig. 2, F1). The Table 1 Sample load in µL on the agarose gel for visualization of crude DNA extracts. pattern for the nitrifying sludge, especially, indicated complete failure of the extraction procedure. The gel image of the crude DNA extraction for procedure E occurred almost similar to procedure D with one exception. The crude DNA extract of the activated sludge showed a slight distinct genomic DNA band, however, the background staining indicated the presence of impurities (Fig. 2, G1). Nevertheless, positive PCR amplification was obtained for the crude DNA extract from activated sludge for procedure E (Fig. 2, G2). Surprisingly, positive amplification of the nitrifying sludge was also obtained for both procedure D and E (Fig. 2, F2). The results of the crude DNA extracts of procedure H and I (method according to [5,6]) are presented in Fig. 3. All crude DNA extracts of procedure H indicate a slight distinct genomic DNA band and higher content of impurities through background staining (Fig. 3, H1). Positive PCR amplification was only obtained for the crude DNA extract of the anaerobic digestion sludge. PCR amplification of the crude DNA extracts of the activated sludge, Havel River sediment and nitrifying sludge failed (Fig. 3, H2). The quality of crude DNA extracts of procedure I was different between the four environmental samples (Fig. 3, I1). A distinct genomic DNA band without higher content of visible impurities was obtained for the activated sludge. The degree of increased impurities occurred slightly for the crude DNA extracts of the Havel River sediment, but a distinct genomic DNA band was still good visible on the gel image. The crude DNA extract of the anaerobic digestion sludge showed higher content of DNA fragmentation as well as possible impurities in the background of the gel. Besides a distinct DNA band higher background smearing was also visible for the crude DNA extract of the nitrifying sludge. Positive PCR amplification was only obtained for the crude DNA extract of the activated sludge (Fig. 3, I2).
The results of the crude DNA extracts of procedure J are presented in Fig. 4 (method according to [7]). The gel image indicated distinct genomic DNA bands with lower content of background smearing for the activated sludge, Havel River sediment and the nitrifying sludge. A higher degree of possible DNA fragmentation and/or background impurities were observed for the crude DNA extract of the anaerobic digestion sludge (Fig. 4, J1). Positive PCR amplification was obtained from the activated sludge, Havel River sediment and the nitrifying sludge, while the amplification for the anaerobic digestion sludge failed (Fig. 4, J2).
The cost analysis of the ten DNA extraction procedures and the two commercial DNA extraction kits is presented in detail in Tables 2-13. Our cost analysis is based on cost estimation. Therefore a cost range between lowest and highest prices is presented. We assumed that the real extraction price will be in this cost range. The presented results show that every extraction procedure has its specific cost range, which is mainly dependent on the extraction time and therefore also on the cost of the laboratory staff. We calculated the lowest laboratory staff cost ranging between 3.65 € and 5.10 € for procedure J (Table 11), and the highest ranging between 8.68 and 12.15 for procedure A ( Table 2). We calculated the lowest cost for the chemicals needed ranging between 0.13 € to 0.31 € for procedure D (Table 5) and the highest cost ranging between 0.47 € to 0.96 € for procedure I (Table 10). The cost for the other consumables such as gloves, tubes and tips were almost similar for all analyzed extraction procedures and extraction kits.

Experimental design, materials and methods
The sample preservation, DNA extraction, PCR performance and gel electrophoresis were described elsewhere [1]. For the cost analysis, a cost range was estimated ranging between minimum and maximum prices for all needed consumables. The number of required tubes and tips per extraction was counted. In all equations that follow, an index was included identifying low or high cost calculations, respectively. For clarification, the letter x represents all low cost calculations and the letter y represents all high cost calculations. The individual cost per chemical needed for every DNA extraction was calculated either with Eqs. (1) or (2), where m extraction is the chemical weight required for a single DNA extraction and m total,fix cost is the total weight corresponding to the fix cost. The individual cost for additional consumables such as gloves, tubes and/or tips was calculated either with Eqs. (3) or (4).
Chemical costs y €=prep Â Ã ¼ m extraction ñFixcost y m total; fixcosty ð2Þ Additional concumable costs x €=prep Additional concumable costs y €=prep Â Ã ¼ Consumbleused extraction ñFixcost y Totalconsumable fixcosty ð4Þ The cost for the lab staff was calculated either with Eqs. (5) or (6). The calculation is based on a total of 12 extractions per staff and the individual extraction time of the tested extraction procedures.
The sum of total costs of chemicals was calculated either with Eqs. (7) or (8). The total costs of all additional consumables needed per extraction was calculated either with Eqs. (9) or (10). The final price per preparation was then calculated either with Eqs. (11) or (12) considering the cost for the lab staff, for all chemicals and additional consumables needed.
Total chemcial costs y €=prep Total additional consumables costs x €=prep Total additional consumables costs y €=prep Final Final price y €=prep Â Ã ¼ Lab staff y þ ∑Chemical costs y þ ∑Additional consumable costs y ð12Þ

Cost analysis
See Tables 2-13.        Table 9 Cost analysis for DNA extraction procedure H (according to Tabatabaei et al. [5]).   Table 11 Cost analysis for DNA extraction procedure J (according to Wilson [7]).