Single cell transcriptome amplification with MALBAC

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Chapman, Alec R ^a,b   He, Zi ^a   Lu, Sijia ^a   Yong, Jun ^c   Tan, Longzhi ^a   Tang, Fuchou ^c   Xie, X Sunney ^a  

^a HARVARD UNIVERSITY   (United States)

^b HARVARD UNIVERSITY   (United States)

^c PEKING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; RNA; TRANSCRIPTOME;

ANIMAL CELL; ANIMAL CELL CULTURE; ARTICLE; CONTROLLED STUDY; EMBRYO; EMBRYONIC STEM CELL; EPITHELIAL MESENCHYMAL TRANSITION; GASTRULATION; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC PROCEDURES; GENOME; MESODERM; MOUSE; MULTIPLE ANNEALING AND LOOPING BASED AMPLIFICATION CYCLES; NONHUMAN; SEQUENCE ANALYSIS; SINGLE CELL TRANSCRIPTOME AMPLIFICATION; ANIMAL; C57BL MOUSE; CELL LINE; GENETICS; GERM LAYER; NUCLEIC ACID AMPLIFICATION; PHYSIOLOGY; PROCEDURES; REPRODUCIBILITY;

ANIMALS; CELL LINE; EPITHELIAL-MESENCHYMAL TRANSITION; GASTRULATION; GERM LAYERS; MICE; MICE, INBRED C57BL; NUCLEIC ACID AMPLIFICATION TECHNIQUES; REPRODUCIBILITY OF RESULTS; TRANSCRIPTOME;

EID: 84926429952     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0120889     Document Type: Article

References (38)

1. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth. 2008; 5: 621-628. doi: 10.1038/nmeth.1226
2. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA Synthesis in Mammalian Cells. PLoS Biol. 2006; 4: e309. doi: 10.1371/journal.pbio.0040309 PMID: 17048983
3. Topalidou I, Oudenaarden A van, Chalfie M. Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression. PNAS. 2011; 108: 4063-4068. doi: 10.1073/pnas.1101329108 PMID: 21368126
4. Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, Hearn J, et al. Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells. Science. 2010; 329: 533-538. doi: 10.1126/science.1188308 PMID: 20671182
5. Warren LA, Rossi DJ, Schiebinger GR, Weissman IL, Kim SK, Quake SR. Transcriptional instability is not a universal attribute of aging. Aging Cell. 2007; 6: 775-782. doi: 10.1111/j.1474-9726.2007.00337.x PMID: 17925006
6. Bengtsson M, Ståhlberg A, Rorsman P, Kubista M. Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res. 2005; 15: 1388-1392. doi: 10.1101/gr.3820805 PMID: 16204192
7. Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, et al. Association of reactive oxygen species levels and radioresistance in cancer stem cells. Nature. 2009; 458: 780-783. doi: 10.1038/nature07733 PMID: 19194462
8. Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. Nat Protocols. 2012; 7: 829-838. doi: 10.1038/nprot.2012.021 PMID: 22481529
9. Guo G, Huss M, Tong GQ, Wang C, Li Sun L, Clarke ND, et al. Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst. Developmental Cell. 2010; 18: 675-685. doi: 10.1016/j.devcel.2010.02.012 PMID: 20412781
10. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, Xu N, et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods. 2009; 6: 377-382. doi: 10.1038/nmeth.1315 PMID: 19349980
11. Tang F, Barbacioru C, Nordman E, Li B, Xu N, Bashkirov VI, et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nature Protocols. 2010; 5: 516-535. doi: 10.1038/nprot.2009.236 PMID: 20203668
12. Raser JM, O'Shea EK. Control of stochasticity in eukaryotic gene expression. Science. 2004; 304: 1811-1814. doi: 10.1126/science.1098641 PMID: 15166317
13. Tang F, Lao K, Surani MA. Development and applications of single-cell transcriptome analysis. Nature Methods. 2011; doi: 10.1038/nmeth.1557
14. Yan L, Yang M, Guo H, Yang L, Wu J, Li R, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013; 20: 1131-1139. doi: 10.1038/nsmb.2660 PMID: 23934149
15. Sasagawa Y, Nikaido I, Hayashi T, Danno H, Uno KD, Imai T, et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biology. 2013; 14: R31. doi: 10.1186/gb-2013-14-4-r31 PMID: 23594475
16. Islam S, Kjällquist U, Moliner A, Zajac P, Fan J-B, Lönnerberg P, et al. Characterization of the singlecell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 2011; 21: 1160-1167. doi: 10.1101/gr.110882.110 PMID: 21543516
17. Islam S, Kjällquist U, Moliner A, Zajac P, Fan J-B, Lönnerberg P, et al. Highly multiplexed and strandspecific single-cell RNA 50 end sequencing. Nat Protocols. 2012; 7: 813-828. doi: 10.1038/nprot.2012.022 PMID: 22753607
18. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, et al. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Meth. 2014; 11: 163-166. doi: 10.1038/nmeth.2772
19. Picelli S, Björklund ÅK, Faridani OR, Sagasser S, Winberg G, Sandberg R. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Meth. 2013; 10: 1096-1098. doi: 10.1038/nmeth.2639
20. Picelli S, Faridani OR, Björklund ÅK, Winberg G, Sagasser S, Sandberg R. Full-length RNA-seq from single cells using Smart-seq2. Nat Protocols. 2014; 9: 171-181. doi: 10.1038/nprot.2014.006 PMID: 24385147
21. Ramsköld D, Luo S, Wang Y-C, Li R, Deng Q, Faridani OR, et al. Full-length mRNA-Seq from singlecell levels of RNA and individual circulating tumor cells. Nature Biotechnology. 2012; 30: 777-782. doi: 10.1038/nbt.2282 PMID: 22820318
22. Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification. Cell Reports. 2012; 2: 666-673. doi: 10.1016/j.celrep.2012.08.003 PMID: 22939981
23. Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, Paul F, Zaretsky I, et al. Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types. Science. 2014; 343: 776-779. doi: 10.1126/science.1247651 PMID: 24531970
24. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells. PNAS. 2013; 110: 594-599. doi: 10.1073/pnas.1217322109 PMID: 23267071
25. Zong C, Lu S, Chapman AR, Xie XS. Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell. Science. 2012; 338: 1622-1626. doi: 10.1126/science.1229164 PMID: 23258894
26. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid Amplification of Plasmid and Phage DNA Using Phi29 DNA Polymerase and Multiply-Primed Rolling Circle Amplification. Genome Res. 2001; 11: 1095-1099. doi: 10.1101/gr.180501 PMID: 11381035
27. Lu S, Zong C, Fan W, Yang M, Li J, Chapman AR, et al. Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing. Science. 2012; 338: 1627-1630. doi: 10.1126/science.1229112 PMID: 23258895
28. Beddington RS., Robertson EJ. Anterior patterning in mouse. Trends in Genetics. 1998; 14: 277-284. doi: 10.1016/S0168-9525(98)01499-1 PMID: 9676530
29. Beddington RS., Robertson EJ. Axis Development and Early Asymmetry in Mammals. Cell. 1999; 96: 195-209. doi: 10.1016/S0092-8674(00)80560-7 PMID: 9988215
30. Lim J, Thiery JP. Epithelial-mesenchymal transitions: insights from. Development. 2012; 139: 3471-3486. doi: 10.1242/dev.071209 PMID: 22949611
31. Nakaya Y, Sheng G. Epithelial to mesenchymal transition during gastrulation: An embryological view. Development, Growth & Differentiation. 2008; 50: 755-766. doi: 10.1111/j.1440-169X.2008.01070.x
32. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 2013; 14: R36. doi: 10.1186/gb-2013-14-4-r36 PMID: 23618408
33. Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotech. 2013; 31: 46-53. doi: 10.1038/nbt.2450
34. Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010; 11: 94. doi: 10.1186/1471-2105-11-94 PMID: 20167110
35. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biology. 2010; 11: R106. doi: 10.1186/gb-2010-11-10-r106 PMID: 20979621
36. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics. 2009; 10: 48. doi: 10.1186/1471-2105-10-48 PMID: 19192299
37. Ciruna B, Rossant J. FGF Signaling Regulates Mesoderm Cell Fate Specification and Morphogenetic Movement at the Primitive Streak. Developmental Cell. 2001; 1: 37-49. doi: 10.1016/S1534-5807(01)00017-X PMID: 11703922
38. Acloque H, Ocaña OH, Matheu A, Rizzoti K, Wise C, Lovell-Badge R, et al. Reciprocal Repression between Sox3 and Snail Transcription Factors Defines Embryonic Territories at Gastrulation. Developmental Cell. 2011; 21: 546-558. doi: 10.1016/j.devcel.2011.07.005 PMID: 21920318