Transcriptome sequencing of the microarray quality control (MAQC) RNA reference samples using next generation sequencing

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Mane, Shrinivasrao P ^a   Evans, Clive ^a   Cooper, Kristal L ^a   Crasta, Oswald R ^a   Folkerts, Otto ^a   Hutchison, Stephen K ^b   Harkins, Timothy T ^c   Thierry Mieg, Danielle ^d   Thierry Mieg, Jean ^d   Jensen, Roderick V ^e  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b 454 Life Sciences Corporation   (United States)

^c Roche Applied Science   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

^e VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENE MAPPING; GENE SEQUENCE; GENETIC DATABASE; HUMAN GENOME; MICROARRAY ANALYSIS; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; COMPARATIVE STUDY; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; HUMAN; METHODOLOGY; QUALITY CONTROL; SEQUENCE ANALYSIS; STANDARD;

COMPLEMENTARY DNA;

DATABASES, GENETIC; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REFERENCE STANDARDS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 67650394369     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-264     Document Type: Article

References (29)

1. Shi L Reid LH Jones WD Shippy R Warrington JA Baker SC Collins PJ de Longueville F Kawasaki ES Lee KY The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nature Biotech 2006, 24(9):1151-1161. 10.1038/ nbt1239
2. Canales RD Luo Y Willey JC Austermiller B Barbacioru CC Boysen C Hunkapiller K Jensen RV Knight CR Lee KY Evaluation of DNA microarray results with quantitative gene expression platforms Nature Biotech 2006, 24(9):1115-1122. 10.1038/nbt1236
3. Wold B Myers RM Sequence census methods for functional genomics Nature Methods 2008, 5:19-21. 10.1038/nmeth1157 18165803
4. Shendure J The beginning of the end for microarrays? Nature Methods 2008, 5(7):585-587. 10.1038/nmeth0708-585 18587314
5. Bainbridge MN Warren RL Hirst M Romanuik T Zeng T Go A Delaney A Griffith M Hickenbotham M Magrini V et al Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach BMC Genomics 2006, 7:246. 1592491 17010196 10.1186/ 1471-2164-7-246
6. Emrich SJ Barbazuk WB Li L Schnable PS Gene discovery and annotation using LCM-454 transcriptome sequencing Genome Res 2007, 17(1):69-73. 1716268 17095711 10.1101/gr.5145806
7. Weber AP Weber KL Carr K Wilkerson C Ohlrogge JB Sampling the Arabidopsis transcriptome with massively parallel pyrosequencing Plant Physiology 2007, 144(1):32-42. 1913805 17351049 10.1104/pp.107.096677
8. Sugarbaker DJ Richards WG Gordon GJ Dong L De Rienzo A Maulik G Glickman JN Chirieac LR Hartman ML Taillon BE et al Transcriptome sequencing of malignant pleural mesothelioma tumors Proc Natl Acad Sci USA 2008, 105(9):3521-3526. 2265129 18303113 10.1073/pnas.0712399105
9. Mao C Evans C Jensen RV Sobral BW Identification of new genes in Sinorhizobium meliloti using the Genome Sequencer FLX system BMC Microbiol 2008, 8:72. 2396165 18454850 10.1186/1471-2180-8-72
10. Nagalakshmi U Wang Z Waern K Shou C Raha D Gerstein M Snyder M The transcriptional landscape of the yeast genome defined by RNA sequencing Science 2008, 320:5881-1344. 1349 10.1126/science.1158441 18451266
11. Wilhelm BT Marguerat S Watt S Schubert F Wood V Goodhead I Penkett CJ Rogers J Bahler J Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution Nature 2008, 453(7199):1239-1243. 10.1038/nature07002 18488015
12. Cloonan N Forrest AR Kolle G Gardiner BB Faulkner GJ Brown MK Taylor DF Steptoe AL Wani S Bethel G et al Stem cell transcriptome profiling via massive-scale mRNA sequencing Nature Methods 2008, 5(7):613-619. 10.1038/ nmeth.1223 18516046
13. Mortazavi A Williams BA McCue K Schaeffer L Wold B Mapping and quantifying mammalian tra0nscriptomes by RNA-Seq Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226 18516045
14. Rosenkranz R Borodina T Lehrach H Himmelbauer H Characterizing the mouse ES cell transcriptome with Illumina sequencing Genomics 2008, 92(4):187-194. 10.1016/j.ygeno.2008.05.011 18602984
15. Morin R Bainbridge M Fejes A Hirst M Krzywinski M Pugh T McDonald H Varhol R Jones S Marra M Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing Biotechniques 2008, 45(1):81-94. 10.2144/000112900 18611170
16. Mudge J Miller NA Khrebtukova I Lindquist IE May GD Huntley JJ Luo S Zhang L van Velkinburgh JC Farmer AD et al Genomic convergence analysis of schizophrenia: MRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum PLoS ONE 2008, 3(11):e3625. 2576459 18985160 10.1371/journal.pone.0003625
17. Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z et al Genome sequencing in microfabricated high-density picolitre reactors Nature 2005, 437(7057):376-380. 1464427 16056220
18. Thierry-Mieg D Thierry-Mieg J AceView: A comprehensive cDNA-supported gene and transcripts annotation Genome Biology 2006, 7(Suppl 1):S12. 11-14 1810549 16925834
19. McClintick JN Edenberg HJ Effects of filtering by Present call on analysis of microarray experiments BMC Bioinformatics 2006, 7:49. 1409797 16448562 10.1186/1471-2105-7-49
20. Graveley BR Power Sequencing Nature 2008, 453:1197-1198. 10.1038/ 4531197b 18580940
21. Sultan M Schulz MH Richard H Magen A Klingenhoff A Scherf M Seifert M Borodina T Soldatov A Parkhomchuk D et al A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome Science 2008, 321(5891):956-960. 10.1126/science.1160342 18599741
22. 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(12):1413-1415. 10.1038/ng.259 18978789
23. Wang ET Sandberg R Luo S Khrebtukova I Zhang L Mayr C Kingsmore SF Schroth GP Burge CB Alternative isoform regulation in human tissue transcriptomes Nature 2008, 456(7221):470-476. 2593745 18978772 10.1038/ nature07509
24. Salehi-Ashtiani K Yang X Derti A Tian W Hao T Lin C Makowski K Shen L Murray RR Szeto D et al Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing Nat Methods 2008, 5(7):597-600. 10.1038/nmeth.1224 18552854
25. Harris TD Buzby PR Babcock H Beer E Bowers J Braslavsky I Causey M Colonell J Dimeo J Efcavitch JW et al Single-molecule DNA sequencing of a viral genome Science 2008, 320(5872):106-109. 10.1126/science.1150427 18388294
26. Lundquist PM Zhong CF Zhao P Tomaney AB Peluso PS Dixon J Bettman B Lacroix Y Kwo DP McCullough E et al Parallel confocal detection of single molecules in real time Opt Lett 2008 33 9 1026 1028 10.1364/ OL.33.001026 18451975
27. Shendure J Porreca GJ Reppas NB Lin X McCutcheon JP Rosenbaum AM Wang MD Zhang K Mitra RD Church GM Accurate multiplex polony sequencing of an evolved bacterial genome Science 2005, 309(5741):1728-1732. 10.1126/ science.1117389 16081699
28. Denoeud F Aury JM Da Silva C Noel B Rogier O Delledonne M Morgante M Valle G Wincker P Scarpelli C et al Annotating genomes with massive-scale RNA sequencing Genome Biol 2008, 9(12):R175. 2646279 19087247 10.1186/gb-2008-9-12-r175
29. Bemmo A Benovoy D Kwan T Gaffney DJ Jensen RV Majewski J Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays BMC Genomics 2008, 9(1):529. 2585104 18990248 10.1186/1471-2164-9-529