The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol
Open accessAbstract
Efficient preparation of high-quality sequencing libraries that well represent the biological sample is a key step for using next-generation sequencing in research. Tn5 enables fast, robust, and highly efficient processing of limited input material while scaling to the parallel processing of hundreds of samples. Here, we present a robust Tn5 transposase purification strategy based on an N-terminal His6-Sumo3 tag. We demonstrate that libraries prepared with our in-house Tn5 are of the same quality as those processed with a commercially available kit (Nextera XT), while they dramatically reduce the cost of large-scale experiments. We introduce improved purification strategies for two versions of the Tn5 enzyme. The first version carries the previously reported point mutations E54K and L372P, and stably produces libraries of constant fragment size distribution, even if the Tn5-to-input molecule ratio varies. The second Tn5 construct carries an additional point mutation (R27S) in the DNA-binding domain. This construct allows for adjustment of the fragment size distribution based on enzyme concentration during tagmentation, a feature that opens new opportunities for use of Tn5 in customized experimental designs. We demonstrate the versatility of our Tn5 enzymes in different experimental settings, including a novel single-cell polyadenylation site mapping protocol as well as ultralow input DNA sequencing.
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Cites
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Full-length RNA-seq from single cells using Smart-seq2
Picelli, S., Faridani, O. R., Björklund, Å. K., Winberg, G., Sagasser, S., & Sandberg, R. (2014) · Nature Protocols · doi:10.1038/nprot.2014.006 · Cited by 4,137
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
Picelli, S., Björklund, Å. K., Faridani, O. R., Sagasser, S., Winberg, G., & Sandberg, R. (2013) · Nature Methods · doi:10.1038/nmeth.2639 · Cited by 2,358 · cited 3×
“…hands-on time, while the end identi fi er allows for speci fi c ampli fi cation of 3 9 ends. mRNA priming and cDNA synthesis were performed as described in Picelli et al. (2013) and tagmentation was performed as described above with a few important modi fi cations (see Figure 4A for a schematic…”
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Wu, T. D., & Nacu, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq057 · Cited by 1,894
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
Nagano, T., Lubling, Y., Stevens, T. J., Schoenfelder, S., Yaffe, E., Dean, W., Laue, E. D., Tanay, A., & Fraser, P. (2013) · Nature · doi:10.1038/nature12593 · Cited by 1,589
Single-cell messenger RNA sequencing reveals rare intestinal cell types
Grün, D., Lyubimova, A., Kester, L., Wiebrands, K., Basak, O., Sasaki, N., Clevers, H., & van Oudenaarden, A. (2015) · Nature · doi:10.1038/nature14966 · Cited by 1,234
Human haematopoietic stem cell lineage commitment is a continuous process
Velten, L., Haas, S. F., Raffel, S., Blaszkiewicz, S., Islam, S., Hennig, B. P., Hirche, C., Lutz, C., Buss, E. C., Nowak, D., et al. (2017) · Nature Cell Biology · doi:10.1038/ncb3493 · Cited by 925
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Baccin, C., Al-Sabah, J., Velten, L., Helbling, P. M., Grünschläger, F., Hernández-Malmierca, P., Nombela-Arrieta, C., Steinmetz, L. M., Trumpp, A., & Haas, S. (2020) · Nature Cell Biology · doi:10.1038/s41556-019-0439-6 · Cited by 904
Self-citationAgeing hallmarks exhibit organ-specific temporal signatures
Schaum, N., Lehallier, B., Hahn, O., Pálovics, R., Hosseinzadeh, S., Lee, S. E., Sit, R., Lee, D. P., Losada, P. M., Zardeneta, M. E., et al. (2020) · Nature · doi:10.1038/s41586-020-2499-y · Cited by 671
A beginner's guide to low‐coverage whole genome sequencing for population genomics
Lou, R. N., Jacobs, A., Wilder, A. P., & Therkildsen, N. O. (2021) · Molecular Ecology · doi:10.1111/mec.16077 · Cited by 334
Triana, S., Vonficht, D., Jopp-Saile, L., Raffel, S., Lutz, R., Leonce, D., Antes, M., Hernández-Malmierca, P., Ordoñez-Rueda, D., Ramasz, B., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01059-0 · Cited by 195
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Metadata
- Authors
- Hennig, B. P., Velten, L., Racke, I., Tu, C. S., Thoms, M., Rybin, V., Besir, H., Remans, K., & Steinmetz, L. M.
- Venue
- G3 Genes|Genomes|Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-01-01
- Volume
- 8
- Issue
- 1
- Pages
- 79-89
- ISSN
- 2160-1836 (ISSN-L)
- OpenAlex
- W2767733991
- Cited by
- 189
- References
- 9
- FWCI
- 4.32
- Type
- journal article
- Language
- en
- Open access
- gold
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- Hennig, B. P., Velten, L., Racke, I., Tu, C. S., Thoms, M., Rybin, V., Besir, H., Remans, K., & Steinmetz, L. M. (2018). Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol. G3 Genes|Genomes|Genetics. https://doi.org/10.1534/g3.117.300257
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
