Counting of RNA molecules using unique molecular identifiers (UMIs) is ubiquitous in single-cell sequencing. Here, we introduce molecular spikes, a new type of RNA spike-ins with in-built UMIs. These versatile molecular spikes have many uses in experimental and computational method development and routine biological applications.
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Ziegenhain, C. et al. Comparative analysis of single-cell RNA sequencing methods. Mol. Cell 65, 631–643 (2017). An article that systematically compared scRNA-seq protocols.
Hagemann-Jensen, M. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat. Biotechnol. 38, 708–714 (2020). This paper reports the development of the Smart-seq3 protocol.
Kanev, K. et al. Tailoring the resolution of single-cell RNA sequencing for primary cytotoxic T cells. Nat. Commun. 12, 569 (2021). An example of a scRNA-seq method with UMI count inflation.
Townes, F. W. & Irizarry, R. A. Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biol. 21, 160 (2020). This article proposes a quasi-UMI method for normalizing read count data.
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This is a summary of: Ziegenhain, C., Hendriks, G.-J., Hagemann-Jensen, M. & Sandberg, R. Molecular spikes: a gold standard for single-cell RNA counting. Nat. Methods https://doi.org/10.1038/s41592-022-01446-x (2022).
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Novel spike-ins for single-cell sequencing enable ground-truth RNA counting. Nat Methods 19, 530–531 (2022). https://doi.org/10.1038/s41592-022-01456-9