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Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps

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Abstract

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.

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Data availability

The raw reads have been uploaded to NCBI under Bioproject Numbers PRJNA749868, PRJNA750567.

Code availability

The custom codes can be found in online version of this article.

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Acknowledgements

We are grateful to Ms. Lifang Peng for helping with collecting water samples.

Funding

This work was supported by “Science and Technology Commission of Shanghai Municipality (19050501900)” and “Shanghai Academy of Environmental Sciences”.

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Authors and Affiliations

  1. Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, 201306, China

    Ying Wang, Hao Yuan, Junman Huang & Chenhong Li

  2. Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, Shanghai Ocean University, Shanghai, 201306, China

    Ying Wang, Hao Yuan, Junman Huang & Chenhong Li

Authors
  1. Ying Wang
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  2. Hao Yuan
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  3. Junman Huang
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  4. Chenhong Li
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Contributions

YW and CL conceived the research plan. YW and JH did the experiments and collected data. YW, HY and JH analyzed the data. YW and CL wrote the draft. All authors edited and approved the final version of the manuscript.

Corresponding author

Correspondence to Chenhong Li.

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Conflict of interest

CL, YW and HY are authors on a patent applied for by Shanghai Ocean University that covers the inline index technology (201811406204.X), and the remaining author (JH) has no financial conflict of interest.

Ethical approval

We followed the guidelines approved by the Ethical Committee of Shanghai Ocean University, China.

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All authors consent to participate.

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Wang, Y., Yuan, H., Huang, J. et al. Inline index helped in cleaning up data contamination generated during library preparation and the subsequent steps. Mol Biol Rep 49, 385–392 (2022). https://doi.org/10.1007/s11033-021-06884-y

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  • DOI: https://doi.org/10.1007/s11033-021-06884-y

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