内联索引有助于清理在文库制备和后续步骤中产生的数据污染。
Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps.
机构信息
Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China.
Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China.
出版信息
Mol Biol Rep. 2022 Jan;49(1):385-392. doi: 10.1007/s11033-021-06884-y. Epub 2021 Oct 29.
BACKGROUND
High-throughput sequencing involves library preparation and amplification steps, which may induce contamination across samples or between samples and the environment.
METHODS
We tested the effect of applying an inline-index strategy, in which DNA indices of 6 bp were added to both ends of the inserts at the ligation step of library prep for resolving the data contamination problem.
RESULTS
Our results showed that the contamination ranged from 0.29 to 1.25% in one experiment and from 0.83 to 27.01% in the other. We also found that contamination could be environmental or from reagents besides cross-contamination between samples.
CONCLUSIONS
Inline-index method is a useful experimental design to clean up the data and address the contamination problem which has been plaguing high-throughput sequencing data in many applications.
背景
高通量测序涉及文库制备和扩增步骤，这些步骤可能会导致样本之间或样本与环境之间的交叉污染。
方法
我们测试了应用内联索引策略的效果，该策略在文库制备的连接步骤中在插入物的两端添加 6 个碱基的 DNA 索引，以解决数据污染问题。
结果
我们的结果表明，在一个实验中，污染程度从 0.29%到 1.25%不等，而在另一个实验中，污染程度从 0.83%到 27.01%不等。我们还发现，污染可能来自环境，也可能来自试剂，而不仅仅是样本之间的交叉污染。
结论
内联索引方法是一种有用的实验设计，可以清理数据并解决高通量测序数据在许多应用中一直存在的污染问题。
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