A platform independent RNA-Seq protocol for the detection of transcriptome complexity

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Calabrese, Claudia ^a   Mangiulli, Marina ^b   Manzari, Caterina ^b   Paluscio, Anna M ^c   Caratozzolo, Mariano F ^c   Marzano, Flaviana ^c   Kurelac, Ivana ^a   D'Erchia, Anna M ^b   D'Elia, Domenica ^c   Licciulli, Flavio ^c   Liuni, Sabino ^c   Picardi, Ernesto ^b   Attimonelli, Marcella ^b   Gasparre, Giuseppe ^a   Porcelli, Anna M ^d   Pesole, Graziano ^b,c   Sbisà, Elisabetta ^c   Tullo, Apollonia ^c  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b UNIVERSITY OF BARI   (Italy)

^c CNR   (Italy)

^d UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

cDNA library preparation; Platform independent RNA seq; RNA seq

Indexed keywords

COMPLEMENTARY DNA; TRANSCRIPTOME;

ACCURACY; ARTICLE; DNA LIBRARY; GENE AMPLIFICATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; HIGH THROUGHPUT SEQUENCING; PYROSEQUENCING; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; VALIDITY;

EUKARYOTA;

ANIMALS; CELL LINE, TUMOR; CHROMOSOME MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HETEROGRAFTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84889053922     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-855     Document Type: Article

References (35)

1. Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform 2010, 11:181-197. 10.1093/bib/bbp046, 19864250.
2. Shendure J, Aiden EL. The expanding scope of DNA sequencing. Nat Biotechnol 2012, 30:1084-1094. 10.1038/nbt.2421, 23138308.
3. Shokralla S, Spall JL, Gibson JF, Hajibabaei M. Next-generation sequencing technologies for environmental DNA research. Mol Ecol 2012, 21:1794-1805. 10.1111/j.1365-294X.2012.05538.x, 22486820.
4. Simon C, Daniel R. Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 2009, 85:265-276. 10.1007/s00253-009-2233-z, 2773367, 19760178.
5. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489:57-74. 10.1038/nature11247, 3439153, 22955616, ENCODE Project Consortium.
6. Forrest AR, Carninci P. Whole genome transcriptome analysis. RNA Biol 2009, 6:107-112. 10.4161/rna.6.2.7931, 19875928.
7. Dong L, Jensen RV, De Rienzo A, Gordon GJ, Xu Y, Sugarbaker DJ, Bueno R. Differentially expressed alternatively spliced genes in Malignant Pleural Mesothelioma identified using massively parallel transcriptome sequencing. BMC Medical Genetics 2009, 10:149. 10.1186/1471-2350-10-149, 2808307, 20043850.
8. Sajnani MR, Patel AK, Bhatt VD, Tripathi AK, Ahir VB, Shankar V, Shah S, Shah TM, Koringa PG, Jakhesara SJ, Joshi CG. Identification of novel transcripts deregulated in buccal cancer by RNA-seq. Gene 2012, 507:152-158. 10.1016/j.gene.2012.07.036, 22846364.
9. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol. 2012, 2012:251364. 3398667, 22829749.
10. Valletti A, Anselmo A, Mangiulli M, Boria I, Mignone F, Merla G, D'Angelo V, Tullo A, Sbisà E, D'Erchia AM, Pesole G. Identification of tumor-associated cassette exons in human cancer through EST-based computational prediction and experimental validation. Mol Cancer 2010, 9:230. 10.1186/1476-4598-9-230, 2941758, 20813049.
11. Ramsköld D, Kavak E, Sandberg R. How to analyze gene expression using RNA-sequencing data. Methods Mol Biol 2012, 802:259-274. 10.1007/978-1-61779-400-1_17, 22130886.
12. Yang KC, Ku YC, Lovett M, Nerbonne JM. Combined deep microRNA and mRNA sequencing identifies protective transcriptomal signature of enhanced PI3Kα signaling in cardiac hypertrophy. Journal of Molecular and Cellular Cardiology 2012, 53:101-112. 10.1016/j.yjmcc.2012.04.012, 3372631, 22580345.
13. Yu ZB, Han SP, Bai YF, Zhu C, Pan Y, Guo XR. microRNA expression profiling in fetal single ventricle malformation identified by deep sequencing. Int J Mol Med 2012, 29:53-60.
14. Gasparre G, Kurelac I, Capristo M, Iommarini L, Ghelli A, Ceccarelli C, Nicoletti G, Nanni P, De Giovanni C, Scotlandi K, Betts CM, Carelli V, Lollini PL, Romeo G, Rugolo M, Porcelli AM. A mutation threshold distinguishes the antitumorigenic effects of the mitochondrial gene MTND1, an oncojanus function. Cancer Res 2011, 71:6220-6229. 10.1158/0008-5472.CAN-11-1042, 21852384.
15. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001, 11:1095-1099. 10.1101/gr.180501, 311129, 11381035.
16. Rodríguez I, Lázaro JM, Blanco L, Kamtekar S, Berman AJ, Wang J, Steitz TA, Salas M, de Vega M. A specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity. Proc Natl Acad Sci U S A 2005, 102:6407-6412. 10.1073/pnas.0500597102, 1088371, 15845765.
17. Paez JG, Lin M, Beroukhim R, Lee JC, Zhao X, Richter DJ, Gabriel S, Herman P, Sasaki H, Altshuler D, Li C, Meyerson M, Sellers WR. Genome coverage and sequence fidelity of φ{symbol}29 polymerase-based multiple strand displacement whole genome amplification. Nucleic Acids Research 2004, 32:e71. 10.1093/nar/gnh069, 419624, 15150323.
18. Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 2008, 9:843-854. 10.1038/nrg2438, 2715827, 18927579.
19. Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep 2012, 1:277-289. 10.1016/j.celrep.2012.01.001, 3368434, 22685694.
20. Klevebring D, Fagerberg L, Lundberg E, Emanuelsson O, Uhlén M, Lundeberg J. Analysis of transcript and protein overlap in a human osteosarcoma cell line. BMC Genomics 2010, 11:684. 10.1186/1471-2164-11-684, 3014981, 21126332.
21. Cheng ZF, Deutscher MP. An important role for RNase R in mRNA decay. Mol Cell 2005, 17:313-318. 10.1016/j.molcel.2004.11.048, 15664199.
22. Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS One 2008, 3:e2803. 10.1371/journal.pone.0002803, 2481391, 18665230.
23. Kriesel JD, Hobbs MR, Jones BB, Milash B, Nagra RM, Fischer KF. Deep Sequencing for the Detection of Virus-Like Sequences in the Brains of Patients with Multiple Sclerosis: Detection of GBV-C in Human Brain. PLoS One 2012, 7:e31886. 10.1371/journal.pone.0031886, 3297595, 22412845.
24. Bonora E, Porcelli AM, Gasparre G, Biondi A, Ghelli A, Carelli V, Baracca A, Tallini G, Martinuzzi A, Lenaz G, Rugolo M, Romeo G. Defective oxidative phosphorylation in thyroid oncocytic carcinoma is associated with pathogenic mitochondrial DNA mutations affecting complexes I and III. Cancer Res. 2006, 66:6087-6096. 10.1158/0008-5472.CAN-06-0171, 16778181.
25. Porcelli AM, Ghelli A, Ceccarelli C, Lang M, Cenacchi G, Capristo M, Pennisi LF, Morra I, Ciccarelli E, Melcarne A, Bartoletti-Stella A, Salfi N, Tallini G, Martinuzzi A, Carelli V, Attimonelli M, Rugolo M, Romeo G, Gasparre G. The genetic and metabolic signature of oncocytic transformation implicates HIF1alpha destabilization. Hum Mol Genet 2010, 19:1019-1032. 10.1093/hmg/ddp566, 20028790.
26. Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM. Sequencing genomes from single cells by polymerase cloning. Nature Biotechnology 2006, 24:680-686. 10.1038/nbt1214, 16732271.
27. Lasken RS, Stockwell TB. Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol 2007, 7:19. 10.1186/1472-6750-7-19, 1855051, 17430586.
28. Richter DC, Ott F, Auch AF, Schmid R, Huson DH. MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One 2008, 3:e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
29. Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005, 21:1859-1875. 10.1093/bioinformatics/bti310, 15728110.
30. Kozarewa I, Ning Z, Quail MA, Sanders MJ, Berriman M, Turner DJ. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes. Nat Methods 2009 April, 6(4):291.
31. Boria I, Boatti L, Pesole G, Mignone F. NGS Trex - Next Generation Sequences Transcriptome profile explorer. BMC Bioinformatics, in press BMC Bioinformatics, in press,
32. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140. 10.1093/bioinformatics/btp616, 2796818, 19910308.
33. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods 2008, 5:621-628. 10.1038/nmeth.1226, 18516045.
34. Rozen S, Skaletsky HJ. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 2000, 132:365-86.
35. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003, 31:3406-3415. 10.1093/nar/gkg595, 169194, 12824337.