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CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method
Abstract
Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.
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“A detailed description and comparison of both approaches for different RNA sequencing protocols (48,49) yielded slight advantages for the latter sequencing approach in small RNA sequencing without affecting the general expression patterns.”
From miRNATissueAtlas2: an update to the human miRNA tissue atlas (2022) · cites this paper as [49]
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Self-citationmiRNATissueAtlas2: an update to the human miRNA tissue atlas
Keller, A., Gröger, L., Tschernig, T., Solomon, J., Laham, O., Schaum, N., Wagner, V., Kern, F., Schmartz, G. P., Li, Y., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab808 · Cited by 143
Self-citationTsai, A. P., Dong, C., Lin, P. B.-C., Oblak, A. L., Viana Di Prisco, G., Wang, N., Hajicek, N., Carr, A. J., Lendy, E. K., Hahn, O., et al. (2023) · Immunity · doi:10.1016/j.immuni.2023.08.008 · Cited by 71
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Metadata
- Authors
- Hahn, O., Fehlmann, T., Zhang, H., Munson, C. N., Vest, R. T., Borcherding, A., Liu, S., Villarosa, C., Drmanac, S., Drmanac, R., Keller, A., & Wyss-Coray, T.
- Affiliations
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, Germany
- MGI, 2904 Orchard Pkwy, San Jose, CA, USA
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-12-02
- Volume
- 49
- Issue
- 2
- Pages
- e11-e11
- ISSN
- 0305-1048
- 1362-4962
- PMC
- PMC7826285
- Cited by
- 16
- References
- 17
- Language
- en
- Funders
- Nan Fung Life Sciences
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