Description

Discover and profile the entire universe of mRNA in any eukaryotic species with mRNA-Seq, utilizing the Genome Analyzer system. With no probes or primers to design, mRNA-Seq delivers unbiased and unparalleled information about the transcriptome.

The simple workflow and Illumina's optimized mRNA-Seq kits allow you to quickly generate full sequence from any poly-A tailed RNA to analyze novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs in one experiment.


Protocols

Kits


Key Publications

  1. Mortazavi A, Williams BA, McCue K, et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat Methods 5: 621-628.
  2. Han X, Wu X, Chung WY, et al. (2009) Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing Proc Natl Acad Sci U S A 106: 12741-12746
  3. Shah SP, Köbel M, Senz J, et al. (2009) Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med 360: 2719-2729
  4. Maher CA, Palanisamy N, Brenner JC, et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing Proc Natl Acad Sci U S A 106: 12353-12358.
View a complete, searchable list of Illumina publications.

Description

Small RNA Discovery and Analysis is a powerful Genome Analyzer application enabling small RNA profiling in any organism without any prior assumptions. Find novel microRNAs, characterize mutations, and analyze the differential expression of all small RNAs in your sample simultaneously.

With the Genome Analyzer, you can query millions of small RNA sequences in each channel of an eight-channel flow cell, and achieve unprecedented sensitivity and dynamic range for rare small RNA discovery and quantification.


Protocols

Kits

Key Publications

  1. Marson A, Levine SS, Cole MF, Frampton GM, Brambrink T, et al. (2008) Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells Cell 134: 521-533.
  2. Rechavi O, Erlich Y, Amram H, Flomenbilt L, Karginov FV, et al. (2009) Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs Genes Dev 23: 1971-1979.
  3. Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, et al. (2009) Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection PLoS One 4: e6349.
  4. Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, et al. (2008) Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells Genome Res 18: 610-21.
 View a complete, searchable list of Illumina publications.

Description

For many applications, such as transcriptome annotation or bacterial transcriptome profiling, it is desirable to generate reads that maintain information about the strandedness of the transcript. Generate large numbers of high quality reads on the Genome Analyzer by using our standard small RNA-Seq kit and the strand-specific mRNA-Seq protocol, and standard Illumina Cluster Generation and Sequencing reagents.


Protocols

Kits


Key Publications

  1. He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW (2008) The antisense transcriptomes of human cells Science 322: 1855-1857.
  2. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis Cell 133: 523-536.
  3. Core LJ, Waterfall JJ, Lis JT (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322: 1845-1848.
  4. Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, et al. (2009) Transcriptome analysis by strand-specific sequencing of complementary DNA Nucleic Acids Res 37(18) e123.
View a complete, searchable list of Illumina publications.

Description

It is becoming increasingly clear that the transcriptome is composed of coding as well as noncoding RNA (ncRNA). Get a more complete picture of what is going on in the transcriptome using the small RNA-Seq sample Prep kit after performing a simple ribosomal RNA reduction, followed by the standard Illumina RNA sequencing protocol using the Genome Analyzer system.


Protocols

Kits


Key Publications

  1. Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, et al. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing Proc Natl Acad Sci U S A 106: 3976-2981.
  2. Babak T, Deveale B, Armour C, Raymond C, Cleary MA, et al. (2008) Global survey of genomic imprinting by transcriptome sequencing Curr Biol 18: 1735-1741.
  3. Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals Nature 458: 223-237.
  4. He Y, Vogelstein B, Velculescu VE, Papadopolous N, Kinzler KW (2008) The antisense transcriptomes of human cells Science 322: 1855-1857.
View a complete, searchable list of Illumina publications.

Description

Paired-End RNA-Seq is a versatile application using 200-500 bp insert, paired end libraries to facilitate discovery applications such as finding gene fusions in cancer and characterizing novel splice isoforms. This application requires the mRNA-Seq Sample Prep Kit with a small modification and standard Illumina Paired-end Cluster Generation and Sequencing reagents for use in the Genome Analyzer system.


Protocols

Contact your local Field Application Scientist or Technical Support for protocol.

Kits


Key Publications

  1. Han X, Wu X, Chung WY, Nekrutenko A, Altman NS, et al. (2009) Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing Proc Natl Acad Sci U S A 106: 12741-12746.
  2. Shah SP, Köbel M, Senz J, Morin RD, Clarke BA, et al.(2009) Mutation of FOXL2 in granulosa-cell tumors of the ovary N Engl J Med 360: 2719-2729.
  3. Maher CA, Palanisamy N, Brenner JC, cao X, Kalyana-Sundaram S, et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing Proc Natl Acad Sci USA 106: 12353-12358.
  4. Birol I, Jackman SD, Nielsen C, Qian JQ, Varhol R, et al. (2009) De novo Transcriptome Assembly with ABySS Bioinformatics.
View a complete, searchable list of Illumina publications.