Benchmarking full-length transcript single cell mRNA sequencing protocols
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Benchmarking full-length transcript single cell mRNA sequencing protocols. / Probst, Victoria; Simonyan, Arman; Pacheco, Felix; Guo, Yuliu; Nielsen, Finn Cilius; Bagger, Frederik Otzen.
In: BMC Genomics, Vol. 23, 860, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Benchmarking full-length transcript single cell mRNA sequencing protocols
AU - Probst, Victoria
AU - Simonyan, Arman
AU - Pacheco, Felix
AU - Guo, Yuliu
AU - Nielsen, Finn Cilius
AU - Bagger, Frederik Otzen
N1 - Publisher Copyright: © 2022, The Author(s).
PY - 2022
Y1 - 2022
N2 - Background: Single cell mRNA sequencing technologies have transformed our understanding of cellular heterogeneity and identity. For sensitive discovery or clinical marker estimation where high transcript capture per cell is needed only plate-based techniques currently offer sufficient resolution. Results: Here, we present a performance evaluation of four different plate-based scRNA-seq protocols. Our evaluation is aimed towards applications taxing high gene detection sensitivity, reproducibility between samples, and minimum hands-on time, as is required, for example, in clinical use. We included two commercial kits, NEBNext® Single Cell/ Low Input RNA Library Prep Kit (NEB®), SMART-seq® HT kit (Takara®), and the non-commercial protocols Genome & Transcriptome sequencing (G&T) and SMART-seq3 (SS3). G&T delivered the highest detection of genes per single cell. SS3 presented the highest gene detection per single cell at the lowest price. Takara® kit presented similar high gene detection per single cell, and high reproducibility between samples, but at the absolute highest price. NEB® delivered a lower detection of genes but remains an alternative to more expensive commercial kits. Conclusion: For the tested kits we found that ease-of-use came at higher prices. Takara can be selected for its ease-of-use to analyse a few samples, but we recommend the cheaper G&T-seq or SS3 for laboratories where a substantial sample flow can be expected.
AB - Background: Single cell mRNA sequencing technologies have transformed our understanding of cellular heterogeneity and identity. For sensitive discovery or clinical marker estimation where high transcript capture per cell is needed only plate-based techniques currently offer sufficient resolution. Results: Here, we present a performance evaluation of four different plate-based scRNA-seq protocols. Our evaluation is aimed towards applications taxing high gene detection sensitivity, reproducibility between samples, and minimum hands-on time, as is required, for example, in clinical use. We included two commercial kits, NEBNext® Single Cell/ Low Input RNA Library Prep Kit (NEB®), SMART-seq® HT kit (Takara®), and the non-commercial protocols Genome & Transcriptome sequencing (G&T) and SMART-seq3 (SS3). G&T delivered the highest detection of genes per single cell. SS3 presented the highest gene detection per single cell at the lowest price. Takara® kit presented similar high gene detection per single cell, and high reproducibility between samples, but at the absolute highest price. NEB® delivered a lower detection of genes but remains an alternative to more expensive commercial kits. Conclusion: For the tested kits we found that ease-of-use came at higher prices. Takara can be selected for its ease-of-use to analyse a few samples, but we recommend the cheaper G&T-seq or SS3 for laboratories where a substantial sample flow can be expected.
KW - Benchmarking
KW - Full-length RNAseq
KW - G&T sequencing
KW - mRNA sequencing technologies
KW - NEB
KW - Single cell
KW - SMART-seq3
KW - Takara
U2 - 10.1186/s12864-022-09014-5
DO - 10.1186/s12864-022-09014-5
M3 - Journal article
C2 - 36581800
AN - SCOPUS:85145124679
VL - 23
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
M1 - 860
ER -
ID: 340541898