A cost effective 5′, selective single cell transcriptome profiling approach with improved UMI design

Nucleic Acids Research

Volumn 45, Issue 7, 2017, Pages

  Arguel, Marie Jeanne ^a   Lebrigand, Kevin ^a   Paquet, Agnès ^a   García, Sandra Ruiz ^a   Zaragosi, Laure Emmanuelle ^a   Barbry, Pascal ^a   Waldmann, Rainer ^a  

^a UNIVERSITÉ CÔTE D'AZUR   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

5' UNTRANSLATED REGION; ACCURACY; ARTICLE; COST CONTROL; COST EFFECTIVENESS ANALYSIS; DNA BARCODING; DNA FRAGMENTATION; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC TRANSCRIPTION; MICROFLUIDICS; PRIORITY JOURNAL; PROCESS OPTIMIZATION; RNA 3' END PROCESSING; SINGLE CELL ANALYSIS; SYSTEMATIC ERROR; TRANSCRIPTOMICS; UNIQUE MOLECULAR IDENTIFIER; WORKFLOW; CELL CULTURE; ECONOMICS; EVALUATION STUDY; GENE EXPRESSION PROFILING; HEK293 CELL LINE; HUMAN; PROCEDURES; SEQUENCE ANALYSIS;

CELLS, CULTURED; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; HEK293 CELLS; HUMANS; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS;

EID: 85019167058     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkw1242     Document Type: Article

References (30)

1. Ramskold, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O.R., Daniels, G.A., Khrebtukova, I., Loring, J.F., Laurent, L.C. et al. (2012) Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol., 30, 777-782.
2. Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., Lennon, N.J., Livak, K.J., Mikkelsen, T.S. and Rinn, J.L. (2014) The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol., 32, 381-386.
3. Treutlein, B., Brownfeld, D.G., Wu, A.R., Neff, N.F., Mantalas, G.L., Espinoza, F.H., Desai, T.J., Krasnow, M.A. and Quake, S.R. (2014) Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature, 509, 371-375.
4. Shalek, A.K., Satija, R., Adiconis, X., Gertner, R.S., Gaublomme, J.T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D. et al. (2013) Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature, 498, 236-240.
5. Pollen, A.A., Nowakowski, T.J., Shuga, J., Wang, X., Leyrat, A.A., Lui, J.H., Li, N., Szpankowski, L., Fowler, B., Chen, P. et al. (2014) Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat. Biotechnol., 32, 1053-1058.
6. Usoskin, D., Furlan, A., Islam, S., Abdo, H., Lonnerberg, P., Lou, D., Hjerling-Leffer, J., Haeggstrom, J., Kharchenko, O., Kharchenko, P.V. et al. (2015) Unbiased classifcation of sensory neuron types by large-scale single-cell RNA sequencing. Nat. Neurosci., 18, 145-153.
7. Zeisel, A., Munoz-Manchado, A.B., Codeluppi, S., Lonnerberg, P., La Manno, G., Jureus, A., Marques, S., Munguba, H., He, L., Betsholtz, C. et al. (2015) Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 347, 1138-1142.
8. Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B.B., Siddiqui, A. et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods, 6, 377-382.
9. Kolodziejczyk, A.A., Kim, J.K., Svensson, V., Marioni, J.C. and Teichmann, S.A. (2015) The technology and biology of single-cell RNA sequencing. Mol. Cell, 58, 610-620.
10. Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., Lonnerberg, P. and Linnarsson, S. (2014) Quantitative single-cell RNA-seq with unique molecular identifers. Nat. Methods, 11, 163-166.
11. Picelli, S., Björklund, A.K., Faridani, O.R., Sagasser, S., Winberg, G. and Sandberg, R. (2013) Smart-seq2 for sensitive full-length transcriptome profling in single cells. Nat. Methods, 10, 1096-1098.
12. Islam, S., Kjallquist, U., Moliner, A., Zajac, P., Fan, J.B., Lonnerberg, P. and Linnarsson, S. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res., 21, 1160-1167.
13. 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) Massively parallel single-cell RNA-Seq for marker-free decomposition of tissues into cell types. Science, 343, 776-779.
14. Hashimshony, T., Senderovich, N., Avital, G., Klochendler, A., de Leeuw, Y., Anavy, L., Gennert, D., Li, S., Livak, K.J., Rozenblatt-Rosen, O. et al. (2016) CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol., 17, 77.
15. Hashimshony, T., Wagner, F., Sher, N. and Yanai, I. (2012) CEL-Seq: single-cell RNA-Seq by multiplexed linear amplifcation. Cell Rep., 2, 666-673.
16. Macosko, E.Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A.R., Kamitaki, N., Martersteck, E.M. et al. (2015) Highly parallel genome-wide expression profling of individual cells using nanoliter droplets. Cell, 161, 1202-1214.
17. Klein, A.M., Mazutis, L., Akartuna, I., Tallapragada, N., Veres, A., Li, V., Peshkin, L., Weitz, D.A. and Kirschner, M.W. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell, 161, 1187-1201.
18. Wu, A.R., Neff, N.F., Kalisky, T., Dalerba, P., Treutlein, B., Rothenberg, M.E., Mburu, F.M., Mantalas, G.L., Sim, S., Clarke, M.F. et al. (2014) Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods, 11, 41-46.
19. Marcet, B., Chevalier, B., Luxardi, G., Coraux, C., Zaragosi, L.-E., Cibois, M., Robbe-Sermesant, K., Jolly, T., Cardinaud, B., Moreilhon, C. et al. (2011) Control of vertebrate multiciliogenesis by miR-449 through direct repression of the Delta/Notch pathway. Nat. Cell Biol., 13, 693-699.
20. Picelli, S., Faridani, O.R., Björklund, A.K., Winberg, G., Sagasser, S. and Sandberg, R. (2014) Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc., 9, 171-181.
21. Picelli, S., Bjorklund, A.K., Reinius, B., Sagasser, S., Winberg, G. and Sandberg, R. (2014) Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res.
22. Wang, Q., Gu, L., Adey, A., Radlwimmer, B., Wang, W., Hovestadt, V., Bähr, M., Wolf, S., Shendure, J., Eils, R. et al. (2013) Tagmentation-based whole-genome bisulfte sequencing. Nat. Protoc., 8, 2022-2032.
23. Ilicic, T., Kim, J.K., Kolodziejczyk, A.A., Bagger, F.O., McCarthy, D.J., Marioni, J.C. and Teichmann, S.A. (2016) Classifcation of low quality cells from single-cell RNA-seq data. Genome Biol., 17, 29.
24. Zajac, P., Islam, S., Hochgerner, H., Lönnerberg, P. and Linnarsson, S. (2013) Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases. PLoS One, 8, e85270.
25. Fu, G.K., Hu, J., Wang, P.-H. and Fodor, S.P.A. (2011) Counting individual DNA molecules by the stochastic attachment of diverse labels. Proc. Natl. Acad. Sci. U.S.A., 108, 9026-9031.
26. Harbers, M., Kato, S., de Hoon, M., Hayashizaki, Y, Carninci, P. and Plessy, C. (2013) Comparison of RNA-or LNA-hybrid oligonucleotides in template-switching reactions for high-speed sequencing library preparation. BMC Genomics, 14, 1-6.
27. Borgstrom, E., Redin, D., Lundin, S., Berglund, E., Andersson, A.F. and Ahmadian, A. (2015) Phasing of single DNA molecules by massively parallel barcoding. Nat. Commun., 6, 7173.
28. Kinde, I., Wu, J., Papadopoulos, N., Kinzler, K.W. and Vogelstein, B. (2011) Detection and quantifcation of rare mutations with massively parallel sequencing. Proc. Natl. Acad. Sci. U.S.A., 108, 9530-9535.
29. Schmidt, W.M. and Mueller, M.W. (1999) CapSelect: A highly sensitive method for 5' CAP-dependent enrichment of full-length cDNA in PCR-mediated analysis of mRNAs. Nucleic Acids Res., 27, e31.
30. Kebschull, J.M. and Zador, A.M. (2015) Sources of PCR-induced distortions in high-throughput sequencing data sets. Nucleic Acids Res., 43, e143.