Accurate expression profiling of very small cell populations

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Gonzalez Roca, Eva ^a   Garcia Albéniz, Xabier ^a,b   Rodriguez Mulero, Silvia ^a   Gomis, Roger R ^a,c   Kornacker, Karl ^d   Auer, Herbert ^a  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b HOSPITAL CLÍNIC   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

^d OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; MESSENGER RNA;

ARTICLE; BIOTINYLATION; CELL COUNT; CELL POPULATION; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA SYNTHESIS; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; QUANTITATIVE ANALYSIS; RNA ANALYSIS; RNA ISOLATION; ANIMAL; BIOLOGICAL MODEL; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENE LIBRARY; HUMAN; LABORATORY DIAGNOSIS; MAGNETISM; METABOLISM; METHODOLOGY; MOUSE; NANOTECHNOLOGY; NUCLEIC ACID HYBRIDIZATION;

ANIMALS; FALSE POSITIVE REACTIONS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; HUMANS; MAGNETICS; MICE; MODELS, BIOLOGICAL; NANOTECHNOLOGY; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 78650847554     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014418     Document Type: Article

References (29)

1. Schena M, Shalon D, Heller R, Chai A, Brown PO, et al. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci U S A 93: 10614-10619.
2. Bainbridge MN, Warren RL, Hirst M, Romanuik T, Zeng T, et al. (2006) Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics 7: 246.
3. Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161.
4. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.
5. Challen GA, Boles N, Lin KK, Goodell MA (2009) Mouse hematopoietic stem cell identification and analysis. Cytometry A 75: 14-24.
6. Zhang P, Zucchelli M, Bruce S, Hambiliki F, Stavreus-Evers A, et al. (2009) Transcriptome profiling of human pre-implantation development. PLoS One 4: e7844.
7. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, et al. (1990) Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A 87: 1663-1667.
8. Viale A, Li J, Tiesman J, Hester S, Massimi A, et al. (2007) Big results from small samples: evaluation of amplification protocols for gene expression profiling. J Biomol Tech 18: 150-161.
9. Nygaard V, Hovig E (2006) Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res 34: 996-1014.
10. Tomlins SA, Mehra R, Rhodes DR, Shah RB, Rubin MA, et al. (2006) Whole transcriptome amplification for gene expression profiling and development of molecular archives. Neoplasia 8: 153-162.
11. Kurn N, Chen P, Heath JD, Kopf-Sill A, Stephens KM, et al. (2005) Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin Chem 51: 1973-1981.
12. Eklund AC, Turner LR, Chen P, Jensen RV, de Feo G, et al. (2006) Replacing cRNA targets with cDNA reduces microarray cross-hybridization. Nat Biotechnol 24: 1071-1073.
13. Clement-Ziza M, Gentien D, Lyonnet S, Thiery JP, Besmond C, et al. (2009) Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics 10: 246.
14. Zhumabayeva B, Diatchenko L, Chenchik A, Siebert PD (2001) Use of SMART-generated cDNA for gene expression studies in multiple human tumors. Biotechniques 30: 158-163.
15. Subkhankulova T, Livesey FJ (2006) Comparative evaluation of linear and exponential amplification techniques for expression profiling at the single-cell level. Genome Biol 7: R18.
16. Iscove NN, Barbara M, Gu M, Gibson M, Modi C, et al. (2002) Representation is faithfully preserved in global cDNA amplified exponentially from sub-picogram quantities of mRNA. Nat Biotechnol 20: 940-943.
17. Kurimoto K, Yabuta Y, Ohinata Y, Ono Y, Uno KD, et al. (2006) An improved single-cell cDNA amplification method for efficient high-density oligonucleotide microarray analysis. Nucleic Acids Res 34: e42.
18. Tang F, Barbacioru C, Wang Y, Nordman E, Lee C, et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat Methods 6: 377-382.
19. Tietjen I, Rihel JM, Cao Y, Koentges G, Zakhary L, et al. (2003) Single-cell transcriptional analysis of neuronal progenitors. Neuron 38: 161-175.
20. Jensen KB, Watt FM (2006) Single-cell expression profiling of human epidermal stem and transit-amplifying cells: Lrig1 is a regulator of stem cell quiescence. Proc Natl Acad Sci U S A 103: 11958-11963.
21. Janes KA, Wang CC, Holmberg KJ, Cabral K, Brugge JS (2010) Identifying single-cell molecular programs by stochastic profiling. Nat Methods 7: 311-317.
22. Tang F, Barbacioru C, Bao S, Lee C, Nordman E, et al. (2010) Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNASeq analysis. Cell Stem Cell 6: 468-478.
23. Benveniste P, Frelin C, Janmohamed S, Barbara M, Herrington R, et al. (2010) Intermediate-term hematopoietic stem cells with extended but time-limited reconstitution potential. Cell Stem Cell 6: 48-58.
24. Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, et al. (2008) Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics 9: 246.
25. Pradervand S, Paillusson A, Thomas J, Weber J, Wirapati P, et al. (2008) Affymetrix Whole-Transcript Human Gene 1.0 ST array is highly concordant with standard 39 expression arrays. Biotechniques 44: 759-762.
26. Wilson CL, Pepper SD, Hey Y, Miller CJ (2004) Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques 36: 498-506.
27. Zeng F, Baldwin DA, Schultz RM (2004) Transcript profiling during preimplantation mouse development. Dev Biol 272: 483-496.
28. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
29. Auer H, Newsom DL, Nowak NJ, McHugh KM, Singh S, et al. (2007) Generesolution analysis of DNA copy number variation using oligonucleotide expression microarrays. BMC Genomics 8: 111.