Skin swabbing protocol to collect DNA samples from small-bodied fish species

Fish species are commonly used as experimental models in the laboratory. DNA is routinely collected from these animals to permit identification of their genotype. The current standard procedure to sample DNA is fin clipping, which involves anaesthetising individuals and removing a portion of the caudal fin. While fin clipping reliably generates good quality DNA samples for downstream applications, there is evidence that it can alter health and welfare, leading to infection and impacting on the fish's behaviour. This in turn can result in greater variation in the data collected. In a recent study we adapted a skin swabbing protocol to collect DNA from small-bodied fish, including sticklebacks and zebrafish, without the use of anaesthetics or sharp instruments. A rayon-tipped swab was used to collect mucus from the flank of the fish which was then used for DNA extraction. We subsequently demonstrated that – compared to fin clipping – skin swabbing triggered fewer changes in stress axis activation and behaviour. We also found that swabbing had a smaller impact on subsequent data collection, potentially allowing smaller sample sizes in experimental groups after using this technique, so reducing animal use. Here we provide a detailed protocol explaining how to collect DNA samples using skin swabs from small laboratory fish. Skin swabbing is a refined technique to collect DNA from fish, with the potential to reduce the number of animals used in experiments as well.鱼类常被用作实验室实验模型，科研人员通常会从这些实验动物体内采集DNA（脱氧核糖核酸）以鉴定其基因型。当前采集DNA的标准流程为剪鳍法（fin clipping）：先将实验个体麻醉，再截取部分尾鳍（caudal fin）。尽管剪鳍法可稳定获取高质量DNA样本以用于下游实验应用，但已有研究证实，该方法会损害实验鱼的健康与福利，引发感染并改变其行为模式，进而导致所采集的实验数据出现更大的变异。在近期一项研究中，我们对皮肤拭子法（skin swabbing）的采样方案进行了优化，无需使用麻醉剂或锋利器械，即可从棘鱼、斑马鱼等小型鱼类体内采集DNA。具体操作是使用带有粘胶纤维头的拭子（rayon-tipped swab）擦拭鱼体侧面的粘液，将其作为DNA提取的样本。后续研究证实，相较于剪鳍法，皮肤拭子法引发的应激轴激活与行为改变程度更低。此外我们还发现，拭子采样法对后续实验数据采集的影响更小，采用该方法后实验组所需的样本量可进一步缩减，从而减少实验动物的使用数量。本数据集提供了一套详细的操作方案，完整说明如何利用皮肤拭子法从小型实验鱼类体内采集DNA样本。皮肤拭子法是一种优化后的鱼类DNA采集技术，同样可有效降低实验动物的使用量。