Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

Nature Protocols

Volumn 7, Issue 5, 2012, Pages 813-828

  Islam, Saiful ^a   Kjällquist, Una ^a   Moliner, Annalena ^a   Zajac, Pawel ^a   Fan, Jian Bing ^b   Lönnerberg, Peter ^a   Linnarsson, Sten ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ALTERNATIVE RNA SPLICING; ARTICLE; DATA ANALYSIS; GENE EXPRESSION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION; SEQUENCE ANALYSIS; TRANSCRIPTION INITIATION SITE;

5' UNTRANSLATED REGIONS; DNA, COMPLEMENTARY; FLOW CYTOMETRY; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS;

EID: 84859621573     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2012.022     Document Type: Article

References (26)

1. Huang, S. Non-genetic heterogeneity of cells in development: more than just noise. Development 136, 3853-3862 (2009).
2. Elowitz, M.B., Levine, A.J., Siggia, E.D. & Swain, P.S. Stochastic gene expression in a single cell. Science 297, 1183-1186 (2002).
3. Li, H.H. et al. Amplification and analysis of DNA sequences in single human sperm and diploid cells. Nature 335, 414-417 (1988).
4. Kurimoto, K. et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res. 34, e42 (2006).
5. Esumi, S. et al. Method for single-cell microarray analysis and application to gene-expression profiling of GABAergic neuron progenitors. Neurosci. Res. 60, 439-451 (2008).
6. Taniguchi, K., Kajiyama, T. & Kambara, H. Quantitative analysis of gene expression in a single cell by qPCR. Nat. Methods 6, 503-506 (2009).
7. Guo, G. et al. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Dev. Cell 18, 675-685 (2010).
8. Tang, F. et al. mRNA-seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
9. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
10. Salimullah, M., Sakai, M., Plessy, C. & Carninci, P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb. Protoc. published online doi:10.1101/pdb.prot5559 (2011).
11. Raj, A., Peskin, C.S., Tranchina, D., Vargas, D.Y. & Tyagi, S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4, e309 (2006).
12. Chubb, J.R., Trcek, T., Shenoy, S.M. & Singer, R.H. Transcriptional pulsing of a developmental gene. Curr. Biol. 16, 1018-1025 (2006).
13. Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
14. Kurimoto, K., Yabuta, Y., Ohinata, Y. & Saitou, M. Global single-cell cDNA amplification to provide a template for representative high-density oligonucleotide microarray analysis. Nat. Protoc. 2, 739-752 (2007).
15. Morris, J., Singh, J.M. & Eberwine, J.H. Transcriptome analysis of single cells. J. Vis. Exp. published online doi:10.3791/2634 (2011).
16. Zhu, Y.Y., Machleder, E.M., Chenchik, A., Li, R. & Siebert, P.D. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30, 892-897 (2001).
17. Levin, J.Z. et al. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7, 709-715 (2010).
18. Kivioja, T. et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat. Methods 9, 72-74 (2012).
19. Maheshri, N. & O'Shea, E.K. Living with noisy genes: how cells function reliably with inherent variability in gene expression. Annu. Rev. Biophys. Biomol. Struct. 36, 413-434 (2007).
20. Tang, F. et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6, 468-478 (2010).
21. Tang, F. et al. Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS ONE 6, e21208 (2011).
22. Dalerba, P. et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nat. Biotechnol. 29, 1120-1127 (2011).
23. Lundin, S., Stranneheim, H., Pettersson, E., Klevebring, D. & Lundeberg, J. Increased throughput by parallelization of library preparation for massive sequencing. PLoS ONE 5, e10029 (2010).
24. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
25. Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876-D882 (2011).
26. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 5, 621-628 (2008).