Normalization of RNA-sequencing data from samples with varying mRNA levels

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Aanes, Håvard ^a   Winata, Cecilia ^b   Moen, Lars F ^a   Østrup, Olga ^c   Mathavan, Sinnakaruppan ^b   Collas, Philippe ^c   Rognes, Torbjørn ^c   Aleström, Peter ^a  

^a NORWEGIAN UNIVERSITY OF LIFE SCIENCES   (Norway)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ACCURACY; ARTICLE; CONTROLLED STUDY; DEVELOPMENTAL STAGE; DNA LIBRARY; EMBRYO; GENE EXPRESSION; NONHUMAN; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ISOLATION; RNA SEQUENCE; ZEBRA FISH; ANIMAL; GENE EXPRESSION PROFILING; GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROCEDURES; SEQUENCE ANALYSIS;

ANIMALS; BASE SEQUENCE; GENE EXPRESSION; GENE EXPRESSION PROFILING; POLYMERASE CHAIN REACTION; RNA, MESSENGER; SEQUENCE ANALYSIS, RNA; ZEBRAFISH;

EID: 84897785776     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0089158     Document Type: Article

References (24)

1. Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, et al. (2011) Synthetic spike-in standards for RNA-seq experiments. Genome Res 21: 1543-1551. gr.121095.111 [pii];10.1101/gr.121095.111 [doi].
2. Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, et al. (2012) A comprehensive evaluation of normalization methods for Illumina highthroughput RNA sequencing data analysis. Brief Bioinform. bbs046 [pii];10.1093/bib/bbs046 [doi].
3. Meyer SU, Pfaffl MW, Ulbrich SE (2010) Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity? Biotechnol Lett 32: 1777-1788. 10.1007/s10529-010-0380-z [doi].
4. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5: 621-628. nmeth.1226 [pii];10.1038/nmeth.1226 [doi].
5. Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25. gb-2010-11-3-r25 [pii];10.1186/gb-2010-11-3-r25 [doi].
6. Aanes H, Winata CL, Lin CH, Chen JP, Srinivasan KG, et al. (2011) Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition. Genome Res 21: 1328-1338. gr.116012.110 [pii];10.1101/gr.116012.110 [doi].
7. Lin CY, Loven J, Rahl PB, Paranal RM, Burge CB, et al. (2012) Transcriptional amplification in tumor cells with elevated c-Myc. Cell 151: 56-67. S0092-8674(12)01057-4 [pii];10.1016/j.cell.2012.08.026 [doi].
8. Konstantinova IM, Kulichkova VA, Vorob'ev VI, Ratovitski EA, Shaposhnikov JD (1977) Studies of poly(A +)-RNA in mouse hepatoma and cortisonestimulated rat liver. Mol Cell Biochem 18: 29-32. (Pubitemid 8234772)
9. Islam S, Kjallquist U, Moliner A, Zajac P, Fan JB, et al. (2011) Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res 21: 1160-1167. gr.110882.110 [pii];10.1101/gr. 110882.110 [doi].
10. van de Peppel J, Kemmeren P, van BH, Radonjic M, van LD, et al. (2003) Monitoring global messenger RNA changes in externally controlled microarray experiments. EMBO Rep 4: 387-393. 10.1038/sj.embor.embor798 [doi];embor798 [pii].
11. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van DS, et al. (2006) Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312: 75-79. 1122689 [pii];10.1126/science.1122689 [doi].
12. Pauli A, Valen E, Lin MF, Garber M, Vastenhouw NL, et al. (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22: 577-591. gr.133009.111 [pii];10.1101/gr.133009.111 [doi].
13. Sagata N, Shiokawa K, Yamana K (1980) A study on the steady-state population of poly(A)+ RNA during early development of Xenopus laevis. Dev Biol 77: 431-448. 0012-1606(80)90486-8 [pii].
14. Piko L, Clegg KB (1982) Quantitative changes in total RNA, total poly(A), and ribosomes in early mouse embryos. Dev Biol 89: 362-378. 0012-1606(82)90325- 6 [pii].
15. Gilbert I, Scantland S, Sylvestre EL, Gravel C, Laflamme I, et al. (2009) The dynamics of gene products fluctuation during bovine pre-hatching development. Mol Reprod Dev 76: 762-772. 10.1002/mrd.21030 [doi].
16. Peaston AE, Graber JH, Knowles BB, de Vries WN (2010) Interrogating the transcriptome of oocytes and preimplantation embryos. Methods Enzymol 477: 481-510. S0076-6879(10)77024-5 [pii];10.1016/S0076-6879(10)77024-5 [doi].
17. Evsikov AV, Marin de EC (2009) Gene expression during the oocyte-to-embryo transition in mammals. Mol Reprod Dev 76: 805-818. 10.1002/mrd.21038 [doi].
18. Loven J, Orlando DA, Sigova AA, Lin CY, Rahl PB, et al. (2012) Revisiting global gene expression analysis. Cell 151: 476-482. S0092-8674(12)01226-3 [pii];10.1016/j.cell.2012.10.012 [doi].
19. Qing T, Yu Y, Du T, Shi L (2013) mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies. Sci China Life Sci 56: 134-142. 10.1007/s11427-013-4437-9 [doi].
20. Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203: 253-310. 10.1002/aja.1002030302 [doi].
21. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408. 10.1006/meth.2001.1262 [doi];S1046-2023(01)91262-9 [pii].
22. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
23. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111. btp120 [pii];10.1093/bioinformatics/btp120 [doi].
24. Vesterlund L, Jiao H, Unneberg P, Hovatta O, Kere J (2011) The zebrafish transcriptome during early development. BMC Dev Biol 11: 30. 1471-213X-11-30 [pii];10.1186/1471-213X-11-30 [doi].