Page 85 - Read Online

Page 18 of 19 Shi et al. J Cancer Metastasis Treat 2018;4:47 I http://dx.doi.org/10.20517/2394-4722.2018.32

88. Hashimshony T, Wagner F, Sher N, Yanai I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep 2012;2:666-73.
89. Kang Y, Norris MH, Zarzycki-Siek J, Nierman WC, Donachie SP, Hoang TT. Transcript amplification from single bacterium for transcrip-
tome analysis. Genome Res 2011;21:925-35.
90. Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, LaMotte RH, Park I-H, Snyder MP, Mason CE, Weiss-
man SM. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A 2013;110:594-
9.
91. Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC. Microfluidic single-cell real-time PCR for comparative analysis of gene expres-
sion patterns. Nat Protoc 2012;7:829.
92. Streets AM, Zhang X, Cao C, Pang Y, Wu X, Xiong L, Yang L, Fu Y, Zhao L, Tang F. Microfluidic single-cell whole-transcriptome sequenc-
ing. Proc Natl Acad Sci U S A 2014;111:7048-53.
93. Toriello NM, Douglas ES, Thaitrong N, Hsiao SC, Francis MB, Bertozzi CR, Mathies RA. Integrated microfluidic bioprocessor for single-
cell gene expression analysis. Proc Natl Acad Sci U S A 2008;105:20173-8.
94. White AK, VanInsberghe M, Petriv I, Hamidi M, Sikorski D, Marra MA, Piret J, Aparicio S, Hansen CL. High-throughput microfluidic
single-cell RT-qPCR. Proc Natl Acad Sci U S A 2011;108:13999-4004.
95. White A, Heyries K, Doolin C, Vaninsberghe M, Hansen C. High-throughput microfluidic single-cell digital polymerase chain reaction.
Anal Chem 2013;85:7182-90.
96. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian D, Zabala M, Bueno J,
Neff NF, Wang J, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, Quake SR. Single-cell dissec-
tion of transcriptional heterogeneity in human colon tumors. Nat Biotechnol 2011;29:1120.
97. Potter NE, Ermini L, Papaemmanuil E, Cazzaniga G, Vijayaraghavan G, Titley I, Ford A, Campbell P, Kearney L, Greaves M. Single-cell
mutational profiling and clonal phylogeny in cancer. Genome Res 2013;23:2115-25.
98. Lawson DA, Bhakta NR, Kessenbrock K, Prummel KD, Yu Y, Takai K, Zhou A, Eyob H, Balakrishnan S, Wang C-Y, Yaswen P, Goga A,
Werb Z. Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells. Nature 2015;526:131.
99. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S. Quantitative single-cell RNA-seq with unique mo-
lecular identifiers. Nat Methods 2014;11:163.
100. Macosko Evan Z, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas Allison R, Kamitaki N, Martersteck Emily M,
Trombetta John J, Weitz David A, Sanes Joshua R, Shalek Alex K, Regev A, McCarroll Steven A. Highly parallel genome-wide expression
profiling of individual cells using nanoliter droplets. Cell 2015;161:1202-14.
101. Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA,
Cepko CL, Regev A, Sanes JR. Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 2016;166:1308-
23.e30.
102. McGranahan N, Burrell RA, Endesfelder D, Novelli MR, Swanton C. Cancer chromosomal instability: therapeutic and diagnostic
challenges:‘Exploring aneuploidy: the significance of chromosomal imbalance’review series. EMBO reports 2012;13:528-38.
103. Bakker B, van den Bos H, Lansdorp PM, Foijer F. How to count chromosomes in a cell: an overview of current and novel technologies.
Bioessays 2015;37:570-7.
104. Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, Martinez P, Philli-
more B, Begum S, Rabinowitz A, Spencer-Dene B, Gulati S, Bates PA, Stamp G, Pickering L, Gore M, Nicol DL, Hazell S, Futreal PA,
Stewart A, Swanton C. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet
2014;46:225.
105. Hughes AEO, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, Eades WC, Elliott K, Heath S, Westervelt P, Ding L, Conrad DF,
White BS, Shao J, Link DC, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Walter MJ, Graubert TA. Clonal architecture of secondary acute
myeloid leukemia defined by single-cell sequencing. PLoS Genet 2014;10:e1004462.
106. Müller S, Liu SJ, Di Lullo E, Malatesta M, Pollen AA, Nowakowski TJ, Kohanbash G, Aghi M, Kriegstein AR, Lim DA. Single-cell se-
quencing maps gene expression to mutational phylogenies in PDGF- and EGF-driven gliomas. Mol Syst Biol 2016;12:889.
107. Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat Genet 2003;33:49.
108. Scheel C, Onder T, Karnoub A, Weinberg RA. Adaptation versus selection: the origins of metastatic behavior. Cancer Res 2007;67:11476-
80.
109. Gawad C, Koh W, Quake SR. Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics. Proc Natl
Acad Sci U S A 2014;111:17947-52.
110. Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S, Li F, Im KM, Wu K, Wu H, Ye X, Li G, Wang L, Zhang B, Liang J, Xie W, Wu R, Jiang H, Liu X,
Yu C, Zheng H, Jian M, Nie L, Wan L, Shi M, Sun X, Tang A, Guo G, Gui Y, Cai Z, Li J, Wang W, Lu Z, Zhang X, Bolund L, Kristiansen K,
Wang J, Yang H, Dean M, Wang J. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-
invasive bladder cancer. GigaScience 2012;1:12.
111. Yu C, Yu J, Yao X, Wu WKK, Lu Y, Tang S, Li X, Bao L, Li X, Hou Y, Wu R, Jian M, Chen R, Zhang F, Xu L, Fan F, He J, Liang Q, Wang H,
Hu X, He M, Zhang X, Zheng H, Li Q, Wu H, Chen Y, Yang X, Zhu S, Xu X, Yang H, Wang J, Zhang X, Sung JJY, Li Y, Wang J. Discovery
of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing. Cell Res 2014;24:701.
112. Jan M, Snyder TM, Corces-Zimmerman MR, Vyas P, Weissman IL, Quake SR, Majeti R. Clonal evolution of preleukemic hematopoietic
stem cells precedes human acute myeloid leukemia. Sci Trans Med 2012;4:149ra18.
113. Wang L, Fan J, Francis JM, Georghiou G, Hergert S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Cin PD, Bowden M, Kotliar D, Shukla
SA, Brown JR, Neuberg D, Alessi DR, Zhang C-Z, Kharchenko PV, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional
analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 2017;27:1300-11.
114. Rhim AD, Thege FI, Santana SM, Lannin TB, Saha TN, Tsai S, Maggs LR, Kochman ML, Ginsberg GG, Lieb JG, Chandrasekhara V,
Drebin JA, Ahmad N, Yang YX, Kirby BJ, Stanger BZ. Detection of circulating pancreas epithelial cells in patients with pancreatic cystic