DNA extraction from African savanna elephant (Loxodonta africana) blood, skin, and dung samples

The aim of this study was to optimise DNA extraction from African savanna elephant blood, skin, and dung samples to obtain DNA of adequate quantity and quality for Oxford Nanopore Sequencing. The effectiveness of non-kit based and kit based DNA extraction and purification methods were investigated. The phenol/chloroform DNA extraction method was of particular interest, and the effect of several modifications to this protocol on the DNA quantity and quality was investigated. Two DNA extraction strategies were investigated for the dung samples, namely: (1) DNA extraction from the surface of the dung, and (2) DNA extraction from membrane filters after performing sequential filtration. This dataset contains information about the date of extraction, sample name, species name, tissue source, amount of tissue, and the DNA extraction or purification method used. NanoDrop spectrophotometry was performed for all samples to obtain the DNA quantity (concentration (ng/µl)) and quality (260/280 and 260/230 ratio). Agarose gel electrophoresis was performed for all samples to determine the presence, intensity, and integrity of the DNA. Qubit fluorometry and TapeStation were done for some samples to determine the DNA concentration (ng/µl) and DNA fragment size, respectively. Polymerase Chain Reaction (PCR) was performed on the DNA extracted from membrane filters after sequential filtration of dung samples. Universal primers were used to detect the presence of bacteria, fungi, plants, nematodes, and vertebrates on each of the filtering levels in the sequential filtration process. The dataset contains the date, sample name, organism to be detected, forward and reverse primer names, expected amplicon size, DNA sample used, PCR reaction, thermocycler conditions, and whether amplification occurred. Agarose gel electrophoresis was performed to determine the presence and size of the amplicons.