Author Correction: Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells (Nature Biotechnology, (2012), 30, 8, (777-782), 10.1038/nbt.2282);Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

Nature Biotechnology

Volumn 30, Issue 8, 2012, Pages 777-782

  Ramsköld, Daniel ^a,b   Luo, Shujun ^c   Wang, Yu Chieh ^d   Li, Robin ^c   Deng, Qiaolin ^a   Faridani, Omid R ^a   Daniels, Gregory A ^e   Khrebtukova, Irina ^c   Loring, Jeanne F ^d   Laurent, Louise C ^f   Schroth, Gary P ^c   Sandberg, Rickard ^a,b  

^a LUDWIG INSTITUTE FOR CANCER RESEARCH   (Sweden)

^b KAROLINSKA INSTITUTE   (Sweden)

^c ILLUMINA INC   (United States)

^d SCRIPPS RESEARCH INSTITUTE   (United States)

^e UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; RNA; TUMORS;

BIOLOGICAL PROBLEMS; CIRCULATING TUMOR CELLS; DIFFERENTIALLY EXPRESSED GENE; GENE EXPRESSION PATTERNS; QUANTITATIVE ACCURACY; SINGLE NUCLEOTIDE POLYMORPHISMS; TRANSCRIPTOME ANALYSIS; TRANSCRIPTOME PROFILING;

CYTOLOGY;

BIOLOGICAL MARKER; MESSENGER RNA; RNA;

ACCURACY; ARTICLE; CELL TYPE; CIRCULATING TUMOR CELL; CONTROLLED STUDY; DILUTION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC IDENTIFICATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; MARKER GENE; MELANOMA; PRIORITY JOURNAL; RNA SEQUENCE; SENSITIVITY ANALYSIS; SINGLE CELL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTOMICS;

EID: 84864880991     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/s41587-020-0427-1     Document Type: Erratum

References (35)

1. Mortazavi, A., Williams, B., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621-628 (2008).
2. Guttman, M. et al. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28, 503-510 (2010).
3. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515 (2010).
4. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
5. Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
6. Kurimoto, K. et al. An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res. 34, e42 (2006).
7. Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods 6, 377-382 (2009).
8. 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).
9. Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
10. Iscove, N.N. et al. Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat. Biotechnol. 20, 940-943 (2002).
11. Katz, Y., Wang, E.T., Airoldi, E.M. & Burge, C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010).
12. Talasaz, A.H. et al. Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device. Proc. Natl. Acad. Sci. USA 106, 3970-3975 (2009).
13. Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 3, 74-79 (2011).
14. Jungbluth, A.A. et al. Expression of melanocyte-associated markers gp-100 and Melan-A/MART-1 in angiomyolipomas. An immunohistochemical and rt-PCR analysis. Virchows Arch. 434, 429-435 (1999).
15. Tomita, Y., Montague, P.M. & Hearing, V.J. Anti-T4-tyrosinase monoclonal antibodies-specific markers for pigmented melanocytes. J. Invest. Dermatol. 85, 426-430 (1985).
16. Fang, D. & Setaluri, V. Role of microphthalmia transcription factor in regulation of melanocyte differentiation marker TRP-1. Biochem. Biophys. Res. Commun. 256, 657-663 (1999).
17. Chomez, P. et al. An overview of the MAGE gene family with the identification of all human members of the family. Cancer Res. 61, 5544-5551 (2001).
18. Tang, A. et al. E-cadherin is the major mediator of human melanocyte adhesion to keratinocytes in vitro. J. Cell Sci. 107, 983-992 (1994).
19. Duncan, L.M. et al. Down-regulation of the novel gene melastatin correlates with potential for melanoma metastasis. Cancer Res. 58, 1515-1520 (1998).
20. Gudbjartsson, D.F. et al. ASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinoma. Nat. Genet. 40, 886-891 (2008).
21. 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).
22. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
23. Ramsköld, D., Wang, E.T., Burge, C.B. & Sandberg, R. An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLOS Comput. Biol. 5, e1000598 (2009).
24. 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. 15, 1388-1392 (2005).
25. Au, K.F., Jiang, H., Lin, L., Xing, Y. & Wong, W.H. Detection of splice junctions from paired-end RNA-seq data by SpliceMap. Nucleic Acids Res. 38, 4570-4578 (2010).
26. Bullard, J.H., Purdom, E., Hansen, K.D. & Dudoit, S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics 11, 94 (2010).
27. Sam, L.T. et al. A comparison of single molecule and amplification based sequencing of cancer transcriptomes. PLoS ONE 6, e17305 (2011).
28. Wall, M.E., Dyck, P.A. & Brettin, T.S. SVDMAN-singular value decomposition analysis of microarray data. Bioinformatics 17, 566-568 (2001).
29. Berger, M.F. et al. Integrative analysis of the melanoma transcriptome. Genome Res. 20, 413-427 (2010).
30. Zawada, A.M. et al. SuperSAGE evidence for CD14.CD16+ monocytes as a third monocyte subset. Blood 118, e50-e61 (2011).
31. Bernstein, B.E. et al. The NIH roadmap epigenomics mapping consortium. Nat. Biotechnol. 28, 1045-1048 (2010).
32. Allison, D.B., Cui, X., Page, G.P. & Sabripour, M. Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. 7, 55-65 (2006).
33. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
34. McKenna, A. et al. The genome analysis toolkit: a mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
35. Sherry, S.T., Ward, M. & Sirotkin, K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 9, 677-679 (1999).