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Items: 20

1.

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.

Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, Owens SM, Betley J, Fraser L, Bauer M, Gormley N, Gilbert JA, Smith G, Knight R.

ISME J. 2012 Aug;6(8):1621-4. doi: 10.1038/ismej.2012.8. Epub 2012 Mar 8.

2.

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.

Quail MA, Smith M, Coupland P, Otto TD, Harris SR, Connor TR, Bertoni A, Swerdlow HP, Gu Y.

BMC Genomics. 2012 Jul 24;13:341. doi: 10.1186/1471-2164-13-341.

3.

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.

Meyer M, Kircher M.

Cold Spring Harb Protoc. 2010 Jun;2010(6):pdb.prot5448. doi: 10.1101/pdb.prot5448.

PMID:
20516186
4.

Single read and paired end mRNA-Seq Illumina libraries from 10 nanograms total RNA.

Sengupta S, Bolin JM, Ruotti V, Nguyen BK, Thomson JA, Elwell AL, Stewart R.

J Vis Exp. 2011 Oct 27;(56):e3340. doi: 10.3791/3340.

5.

Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip.

Thirlwell C, Eymard M, Feber A, Teschendorff A, Pearce K, Lechner M, Widschwendter M, Beck S.

Methods. 2010 Nov;52(3):248-54. doi: 10.1016/j.ymeth.2010.04.012. Epub 2010 Apr 29. Review.

PMID:
20434562
6.

Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes.

Oyola SO, Otto TD, Gu Y, Maslen G, Manske M, Campino S, Turner DJ, Macinnis B, Kwiatkowski DP, Swerdlow HP, Quail MA.

BMC Genomics. 2012 Jan 3;13:1. doi: 10.1186/1471-2164-13-1.

7.

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.

Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM.

Nucleic Acids Res. 2010 Apr;38(6):1767-71. doi: 10.1093/nar/gkp1137. Epub 2009 Dec 16. Review.

8.

A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.

Sultan M, Dökel S, Amstislavskiy V, Wuttig D, Sültmann H, Lehrach H, Yaspo ML.

Biochem Biophys Res Commun. 2012 Jun 15;422(4):643-6. doi: 10.1016/j.bbrc.2012.05.043. Epub 2012 May 15.

9.

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT.

PLoS One. 2012;7(2):e30087. doi: 10.1371/journal.pone.0030087. Epub 2012 Feb 10. Erratum in: PLoS One. 2012;7(3):10.1371/annotation/64ba358f-a483-46c2-b224-eaa5b9a33939.

10.

Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.

11.

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.

Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, Jaffrézic F; French StatOmique Consortium.

Brief Bioinform. 2013 Nov;14(6):671-83. doi: 10.1093/bib/bbs046. Epub 2012 Sep 17.

12.

Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end illumina reads.

Bartram AK, Lynch MD, Stearns JC, Moreno-Hagelsieb G, Neufeld JD.

Appl Environ Microbiol. 2011 Jun;77(11):3846-52. doi: 10.1128/AEM.02772-10. Epub 2011 Apr 1. Erratum in: Appl Environ Microbiol. 2011 Aug;77(15):5569.

13.

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing.

Xiong X, Frank DN, Robertson CE, Hung SS, Markle J, Canty AJ, McCoy KD, Macpherson AJ, Poussier P, Danska JS, Parkinson J.

PLoS One. 2012;7(4):e36009. doi: 10.1371/journal.pone.0036009. Epub 2012 Apr 27.

14.

Illumina-based analysis of microbial community diversity.

Degnan PH, Ochman H.

ISME J. 2012 Jan;6(1):183-94. doi: 10.1038/ismej.2011.74. Epub 2011 Jun 16.

15.

A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq.

Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP.

PLoS One. 2011;6(10):e26426. doi: 10.1371/journal.pone.0026426. Epub 2011 Oct 19. Erratum in: PLoS One. 2011;6(11). doi: 10.1371/annotation/e5ef7afc-7e81-4053-8670-1bb3402f63fd.

16.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

Lazarevic V, Whiteson K, Huse S, Hernandez D, Farinelli L, Osterås M, Schrenzel J, François P.

J Microbiol Methods. 2009 Dec;79(3):266-71. doi: 10.1016/j.mimet.2009.09.012. Epub 2009 Sep 29.

17.

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.

Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT.

ISME J. 2012 Jul;6(7):1273-6. doi: 10.1038/ismej.2011.186. Epub 2011 Dec 15. No abstract available.

18.

Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc.

Roessler J, Ammerpohl O, Gutwein J, Hasemeier B, Anwar SL, Kreipe H, Lehmann U.

BMC Res Notes. 2012 Apr 30;5:210. doi: 10.1186/1756-0500-5-210.

19.

A large genome center's improvements to the Illumina sequencing system.

Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ.

Nat Methods. 2008 Dec;5(12):1005-10. doi: 10.1038/nmeth.1270.

20.

Strategy for microbiome analysis using 16S rRNA gene sequence analysis on the Illumina sequencing platform.

Ram JL, Karim AS, Sendler ED, Kato I.

Syst Biol Reprod Med. 2011 Jun;57(3):162-70. doi: 10.3109/19396368.2011.555598. Epub 2011 Mar 1.

PMID:
21361774
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