Nygaard V, Løland A, Holden M, Langaas M, Rue H, Liu F, et al. Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance. BMC Genomics. 2003;4:11.
Article
Google Scholar
Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Meth. 2008;5:621–8.
Article
CAS
Google Scholar
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
Article
CAS
Google Scholar
Streelman JT, Kocher TD. From phenotype to genotype. Evol Dev. 2000;2:166–73.
Article
CAS
Google Scholar
Kurn N. Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications. Clin Chem. 2005;51:1973–81.
Article
CAS
Google Scholar
López-Maury L, Marguerat S, Bähler J. Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet. 2008;9:583–93.
Article
Google Scholar
Minoche AE, Dohm JC, Himmelbauer H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 2011;12:R112.
Article
CAS
Google Scholar
Fietz J, Tataruch F, Dausmann K, Ganzhorn J. White adipose tissue composition in the free-ranging fat-tailed dwarf lemur (Cheirogaleus medius; Primates), a tropical hibernator. J Comp Physiol B. 2003;173:1–10.
CAS
Google Scholar
Feeney EJ, Austin S, Chien Y-H, Mandel H, Schoser B, Prater S, et al. The value of muscle biopsies in Pompe disease: identifying lipofuscin inclusions in juvenile-and adult-onset patients. Acta Neuropathol Commun. 2014;2:2.
Article
Google Scholar
Hennessey JV, Chromiak JA, Dellaventura S, Guertin J, Maclean DB. Increase in percutaneous muscle biopsy yield with a suction-enhancement technique. J Appl Physiol. 1997;82:1739–42.
CAS
Google Scholar
Barber LJ, Sandhu S, Chen L, Campbell J, Kozarewa I, Fenwick K, et al. Secondary mutations in BRCA2associated with clinical resistance to a PARP inhibitor. J Pathol. 2013;229:422–9.
Article
CAS
Google Scholar
Wang E. RNA amplification for successful gene profiling analysis. J Transl Med. 2005;3:28.
Article
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6:1621–4.
Article
CAS
Google Scholar
Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM. High-fidelity mRNA amplification for gene profiling. Nat Biotechnol. 2000;18:457–9.
Article
CAS
Google Scholar
Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, et al. Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nat Genet. 2012;45:12–7.
Article
Google Scholar
Liu P, Morrison C, Wang L, Xiong D, Vedell P, Cui P, et al. Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. Carcinogenesis. 2012;33:1270–6.
Article
Google Scholar
Eberwine J, Yeh H, Miyashiro K, Cao Y, Nair S, Finnell R, et al. Analysis of gene expression in single live neurons. Proc Natl Acad Sci U S A. 1992;89:3010–4.
Article
CAS
Google Scholar
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A. 1990;87:1663–7.
Article
Google Scholar
Macaulay IC, Voet T. Single cell genomics: advances and future perspectives. PLoS Genet. 2014;10:e1004126.
Article
Google Scholar
Baugh LR, Hill AA, Brown EL, Hunter CP. Quantitative analysis of mRNA amplification by in vitro transcription. Nuc Acids Res. 2001;29:E29.
Article
CAS
Google Scholar
Clément-Ziza M, Gentien D, Lyonnet S, Thiery J-P, Besmond C, Decraene C. Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling. BMC Genomics. 2009;10:246.
Article
Google Scholar
Rudnicki M, Eder S, Schratzberger G, Mayer B, Meyer TW, Tonko M, et al. Reliability of T7-based mRNA linear amplification validated by gene expression analysis of human kidney cells using cDNA microarrays. Nephron Exp Nephrol. 2004;97:e86–95.
Article
CAS
Google Scholar
Scheidl SJ, Nilsson S, Kalén M, Hellström M, Takemoto M, Håkansson J, et al. mRNA expression profiling of laser microbeam microdissected cells from slender embryonic structures. Am J Pathol. 2002;160:801–13.
Article
CAS
Google Scholar
Klur S, Toy K, Williams MP, Certa U. Evaluation of procedures for amplification of small-size samples for hybridization on microarrays. Genomics. 2004;83:508–17.
Article
CAS
Google Scholar
Viale A, Li J, Tiesman J, Hester S, Massimi A, Griffin C, et al. Big results from small samples: evaluation of amplification protocols for gene expression profiling. J Biomol Tech. 2007;18:150–61.
Google Scholar
Gold D, Coombes K, Medhane D, Ramaswamy A, Ju Z, Strong L, et al. A comparative analysis of data generated using two different target preparation methods for hybridization to high-density oligonucleotide microarrays. BMC Genomics. 2004;5:2.
Article
Google Scholar
Zheng W, Chung LM, Zhao H. Bias detection and correction in RNA-Sequencing data. BMC Bioinformatics. 2011;12:290.
Article
CAS
Google Scholar
Shanker S, Paulson A, Edenberg HJ, Peak A, Perera A, Alekseyev YO, Beckloff N, Bivens NJ, Donnelly R, Gillaspy AF, Grove D, Gu W, Jafari N, Kerley-Hamilton JS, Lyons RH, Tepper C, Nicolet CM: Evaluation of Commercially Available RNA Amplification Kits for RNA Sequencing Using Very Low Input Amounts of Total RNA. J Biomol Tech. 2015 Apr;26(1):4-18. doi: 10.7171/jbt.15-2601-001
Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nature Biotechnol. 2011;29:572–3.
Article
CAS
Google Scholar
Liu Y, Zhou J, White KP. RNA-seq differential expression studies: more sequence or more replication? Bioinformatics. 2014;30:301–4.
Article
CAS
Google Scholar
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:516–20.
Article
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014;31:166–9.
Article
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol. 2010;11:R106.
Article
CAS
Google Scholar
Tariq MA, Kim HJ, Jejelowo O, Pourmand N. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nuc Acids Res. 2011;39:e120–e120.
Article
CAS
Google Scholar
Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, Koritala S, et al. Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques. 2004;37:854–7.
CAS
Google Scholar
Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 2008;18:1509–17.
Article
CAS
Google Scholar
Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, et al. The developmental transcriptome ofDrosophila melanogaster. Nature. 2012;471:473–9.
Article
Google Scholar
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, et al. Highly integrated single-base resolution maps of the Epigenome in Arabidopsis. Nuc Acids Res. 2009;133:e123–e123.
Google Scholar
Cloonan N, Forrest ARR, Kolle G, Gardiner BBA, Faulkner GJ, Brown MK, et al. Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Meth. 2008;5:613–9.
Article
CAS
Google Scholar
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008;40:1413–5.
Article
CAS
Google Scholar
Morozova O, Marra MA: Applications of next-generation sequencing technologies in functional genomics. Genomics 2008;92:255–264. doi:10.1016/j.ygeno.2008.07.001
Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008;320:1344–9.
Article
CAS
Google Scholar
Rowley JW, Oler AJ, Tolley ND, Hunter BN, Low EN, Nix DA, et al. Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes. Blood. 2011;118:e101–11.
Article
CAS
Google Scholar
Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, et al. Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature. 2008;453:1239–43.
Article
CAS
Google Scholar
Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009;19:657–66.
Article
CAS
Google Scholar
Daines B, Wang H, Wang L, Li Y, Han Y, Emmert D, et al. The Drosophila melanogaster transcriptome by paired-end RNA sequencing. Genome Res. 2011;21:315–24.
Article
CAS
Google Scholar
Oshlack A, Robinson MD, Young MD. From RNA-seq reads to differential expression results. Genome Biol. 2010;11:220.
Article
CAS
Google Scholar
Ekblom R, Galindo J. Applications of next generation sequencing in molecular ecology of non-model organisms. Heredity. 2010;107:1–15.
Article
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Article
CAS
Google Scholar
Cahais V, Gayral P, Tsagkogeorga G, Melo-Ferreira J, Ballenghien M, Weinert L, et al. Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Mol Ecol Resour. 2012;12:834–45.
Article
CAS
Google Scholar
Deutscher MP. The metabolic role of RNases. Trends Biochem Sci. 1988;13:136–9.
Article
CAS
Google Scholar
Stevens A. Ribonucleic acids: biosynthesis and degradation. Annu Rev Plant Physiol Plant Mol Biol. 1963;32:15–42.
CAS
Google Scholar
Gopee NV, Howard PC. A time course study demonstrating RNA stability in postmortem skin. Exp Mol Pathol. 2007;83:4–10.
Article
CAS
Google Scholar
Ohashi Y, Creek KE, Pirisi L, Kalus R, Young SR. RNA degradation in human breast tissue after surgical removal: a time-course study. Exp Mol Pathol. 2004;77:98–103.
Article
CAS
Google Scholar
Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol. 2006;7:3.
Article
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
Google Scholar
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes inthe presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
Article
Google Scholar
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnol. 2013;31:46–53.
Article
CAS
Google Scholar
Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012;28:2184–5.
Article
CAS
Google Scholar