Characterization of in vitro transcription amplification linearity and variability in the low copy number regime using External RNA Control Consortium (ERCC) spike-ins

Analytical and Bioanalytical Chemistry

Volumn 405, Issue 1, 2013, Pages 315-320

  Kralj, Jason G ^a   Salit, Marc L ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Amplification bias; ERCC; In vitro transcription; RNA amplification

Indexed keywords

ANTISENSE RNA; COPY NUMBER; DETECTION LIMITS; DIFFERENTIAL GENE EXPRESSIONS; ERCC; GENE EXPRESSION PROFILES; IN-VITRO; INPUT SAMPLE; QUANTITATIVE REVERSE TRANSCRIPTION-POLYMERASE CHAIN REACTION; SMALL SAMPLES; SYSTEMATIC BIAS;

GENE EXPRESSION; MAMMALS; POLYMERASE CHAIN REACTION;

RNA;

COMPLEMENTARY RNA; MESSENGER RNA; PRIMER DNA; RNA;

ARTICLE; CHEMICAL ANALYSIS; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; HUMAN; LEUKEMIA CELL LINE; METABOLISM; METHODOLOGY; NUCLEIC ACID AMPLIFICATION; REGRESSION ANALYSIS; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

CHEMISTRY TECHNIQUES, ANALYTICAL; DNA PRIMERS; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; JURKAT CELLS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; RNA, ANTISENSE; RNA, MESSENGER; TRANSCRIPTION, GENETIC;

MAMMALIA;

EID: 84872326444     PISSN: 16182642     EISSN: 16182650     Source Type: Journal    
DOI: 10.1007/s00216-012-6445-1     Document Type: Article

References (17)

1. Hartwell LH, Hopfield JJ, Liebler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52
2. 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
3. Ozsolak F, Ting DT, Wittner BS, Brannigan BW, Paul S, Bardeesy N, Ramaswamy S, Milos PM, Haber DA (2010) Amplification-free digital gene expression profiling from minute cell quantities. Nat Meth 7:619-622
4. Ozsolak F, Milos PM (2010) RNA sequencing: advances, challenges, and opportunities. Nat Rev Genet 12:87-98
5. Kurimoto K, Saitou M (2010) Single-cell cDNA microarray profiling of complex biological processes of differentiation. Curr Op Genet Devel 20:470-477
6. van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH (1990) Amplified RNA synthesized form limited quantities of heterogeneous cDNA. PNAS 87:1663-1667
7. Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM (2000) High-fidelity mRNA amplification for gene profiling. Nat Biotech 18:457-459
8. Baugh LR, Hill AA, Brown EL, Hunter CP (2001) Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res 29:e29
9. Reid LH, Lucas AB, Kopf-Sill AR, Chen B, Bromley B, Foy C, Hinkel CS, Boysen C, Liu CM, Ranamukha-arachchi D, Wagar E, Kawasaki ES, Goodsaid FM, Wilmer F, Fischer G, Kiser GL, Causton HC, Fuscoe JC, Brenton JD, Warrington JA, Soriano J, Coller J, Burrill JD, Rhodes K, Kerr KF, Zoon KC, Lee K, Shi LM, Salit M, Satterfield M, Marton M, Cronin M, Conley MP, Williams M, Fero M, Wilson M, Novoradovskaya N, Gilles P, Wolber PK, Ikonomi P, Puri R, Beyer RP, Shippy R, Setterquist R, Elespuru RK, Baker SC, Chervitz SA, Bauer SR, Russell S, Kaysser-Kranich T, Bammler TK, Ryder TB, Sendera TJ, Scherf U, Gao XL, Wu XN, Guo X, Liu ZL (2005) Proposed methods for testing and selecting the ERCC external RNA controls. BMC Genomics 6:150
10. Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, Causton H, Conley MP, Elespuru R, Fero M, Foy C, Fuscoe J, Gao XL, Gerhold DL, Gilles P, Goodsaid F, Guo X, Hackett J, Hockett RD, Ikonomi P, Irizarry RA, Kawasaki ES, Kaysser-Kranich T, Kerr K, Kiser G, Koch WH, Lee KY, Liu CM, Liu ZL, Lucas A, Manohar CF, Miyada G, Modrusan Z, Parkes H, Puri RK, Reid L, Ryder TB, Salit M, Samaha RR, Scherf U, Sendera TJ, Setterquist RA, Shi LM, Shippy R, Soriano JV, Wagar EA, Warrington JA, Williams M, Wilmer F, Wilson M, Wolber PK, Wu XN, Zadro R (2005) The external RNA controls consortium: a progress report. Nat Methods 2:705-731
11. Devonshire AS, Elaswarapu R, Foy CA (2011) Applicability of RNA standards for evaluating RT-qPCR assays and platforms. BMC Genomics 12:118
12. Nygaard V, Holdin M, Løland A, Langaas M, Myklebost O, Hovig E (2005) Limitations of mRNA amplification from small-size cell samples. BMC Genomics 6:147-163
13. Hansen KD, Brenner SE, Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38:e131
14. Zhang J, Byrne CD (1999) Differential priming of RNA templates during cDNA synthesis markedly affects both accuracy and reproducibility of quantitative competeitive reverse-transcriptase PCR. Biochem J 337:231-241
15. Thompson M (2004) The amazing Horwitz function. AMC Tech Brief
16. Arnold S, Siemann M, Scharnweber K, Werner M, Baumann S, Reuss M (2000) Kinetic modeling and simulation of in vitro transcription by phage T7 RNA polymerase. Biotech Bioeng 72:548-561
17. Submramanian A, Yamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102:15545-15550