Description

Discover and profile the entire mRNA universe with Illumina's mRNA-Seq. With no probes or primers to design, mRNA-Seq delivers unbiased and unparalleled information about the transcriptome.

Quickly generate full sequence from any poly-A tailed RNA with the simple and cost-effective TruSeq RNA Sample Prep kit to analyze novel transcripts, novel isoforms, alternative splice sites, rare transcripts, and cSNPs in one experiment.

 

Kits

For mRNA-Seq Sample Prep:

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):

Protocols


Literature


Key Publications

  1. Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, et al. (2010) Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-Seq Genome Res 20: 1451-1458.
  2. Lu T, Lu G, Fan D, Zhu C, Li W, et al. (2010) Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-Seq Genome Res 20:1238-1249.
  3. Pickrell J, Marioni JC, Pai AA, Degner JF, Engelhardt BE, et al. (2010) Understanding mechanisms underlying human gene expression variation with RNA sequencing Nature 464:768-772.
  4. van Bakel H, Nislow C, Blencowe BJ, and TR Hughes. (2010)  Most "dark matter" transcripts are associated with known genes PLoS Biology 8:e1000371.
View a complete, searchable list of Illumina publications.

Description

As next-generation sequencing continues to evolve and enable tremendous output,  the throughput and multiplexing capabilities of Illumina sequencing-based methods for small RNA analysis have been rapidly adopted for examining gene regulation at the transcriptional and post-transcriptional levels.

Query thousands of small RNA sequences  in each channel of an eight-channel flow cell with unprecedented sensitivity and dynamic range for both small RNA discovery and profiling applications. Find novel microRNAs, characterize variation such as isomirs with single-base resolution, and analyze the differential expression of all small RNAs in any sample without prior assumptions.

 

Kits

For mRNA-Seq Sample Prep:

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):

Protocols


Key Publications

  1. Zhou L, Chen J, Li Z, Li X, Hu X et al. (2010) Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal carcinoma PLoS One 5:e15224.
  2. Xu G, Wu J, Zhou L, Chen B, Sun Z, et al. (2010) Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer line by deep sequencing PLoS One 11:e15519.
  3. Jima D, Zhang J, Jacobs C, Richards KL, Dunphy C, et al. (2010) Deep sequencing of the small transcriptome of normal and malignant B cells identifies hundreds of novel microRNAs Blood 23:e118-127.
  4. 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.
View a complete, searchable list of Illumina publications.

Description

Maintaining transcript strandedness can enhance the value of RNA-Seq for many applications such as transcriptome annotation and bacterial transcriptome profiling. Generate directional libraries for large numbers of high quality reads using the directional (strand-specific) mRNA-Seq Sample Prep protocol.

The Directional mRNA-Seq Sample Prep protocol is an experimental application of Illumina technology, requiring Illumina small RNA sequencing primers and the mRNA-Seq Sample Prep kit. This protocol is compatible with single-read flow cells only.

 

Kits

For Strand-Specific RNA-Seq Sample Prep (both kits required):

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):

Protocols


Key Publications

  1. Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, et al. (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods Nature Methods 9:709-715.
  2. Vivancos AP, Guell M, Dohm JC, Serrano L, Himmelbauer H (2009) Strand-specific deep sequencing of the transcriptome Genome Res 20(7):989-999.
  3. Parkhomchuk D, Amstislavsky V, Soldatov A, Ogryzko V, et al. (2009) Use of high throughput sequencing to observe genome dynamics at a single cell level Proc Natl Acad Sci USA 106(49):20830-5.
  4. Perkins TT, Kingsley RA, Fookes MC, Gardner PP, and James KD (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi PLoS Genet 5(7)e1000569.
View a complete, searchable list of Illumina publications.

Description

Increasing evidence suggests that noncoding RNAs (ncRNA) perform important regulatory functions. Discover and profile genome-wide ncRNA transcripts in any sample, including analysis of highly degraded RNA from FFPE samples, by performing a simple cDNA normalization protocol prior to cluster generation and sequencing.

Duplex-specific thermostable nuclease (DSN) degrades abundant DNA molecules in sequencing sample preparations derived from ribosomal RNA, transfer RNA, and housekeeping genes while preserving DNA derived from less-abundant transcripts. The DSN protocol is an experimental application of Illumina technology, requiring a DSN Kit available from Evrogen, and the Illumina mRNA Sample Prep Kit.

Kits

For mRNA-Seq Sample Prep (both required):

For Directional mRNA-Seq Sample Prep (both required):

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):


Protocols


Key Publications

  1. Jung CH, Hansen MA, Makunin IV, Korbie DJ, Mattick JS (2010) Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data BMC Genomics 11:77.
  2. Wurtzel O, Sapra R, Chen F, Zhu Y, Simmons B, et al. (2010) A single-base resolution map of an archaeal transcriptome Genome Res 20: 133-141.
  3. Erhard F and R Zimmer (2010) Classification of ncRNAs using position and size information in deep sequencing data Bioinformatics 26(18):1426-32.
  4. Olivier H, Orsi RH, Ponnala L, keich U, Wang W, et al. (2009) Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs BMC Genomics 10:641.
View a complete, searchable list of Illumina publications.

Description

For discovery applications such as detecting gene fusions in cancer and characterizing novel splice isoforms, Paired-End RNA-Seq is a versatile application using 200-500 bp insert, paired-end libraries. Use the TruSeq RNA Sample Prep Kit with an alternate fragmentation method, followed by standard Illumina paired-end cluster generation and sequencing.


Kits

For Paired-End mRNA-Seq Sample Prep:

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):

Protocols


Key Publications

  1. Pfleuger D, Terry S, Sboner A, Habegger L, Esgueva R, et al. (2011) Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing Genome Res 1:56-67.
  2. Berger M, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, et al. (2011) The genomic complexity of primary human prostate cancer Nature 470:214-220.
  3. Wang Z, Fang B, Chen J, Zhang X, Luo Z, et al. (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas) BMC Genomics 11:726-739.
  4. Trapnell C, Williams B, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nat Biotechnol 5: 421-423.
View a complete, searchable list of Illumina publications.

Clontech SMARTerTM Ultra Low RNA Kit for Illumina Sequencing

The Clontech SMARTer Ultra Low RNA Kit enables RNA sequencing from exceedingly low amounts of total RNA, starting with as little as 100 pg total RNA. Transcriptome sequencing has been established as a powerful tool for measuring gene expression levels, alternatively spiced isoforms, and gene discovery. This new assay offers the powerful attributes of RNA-Seq with unparalleled sensitivity, accurate gene quantification, and dynamic range.

Using an optimized version of Clontech's SMARTer™ technology, the assay provides an exceptionally efficient method for accurately synthesizing full-length cDNA from RNA in a single reaction. The resulting cDNA is fed directly into Illumina's proven paired-end sample prep kit. The combination of these technologies results in robust sample prep for use on all Illumina sequencing platforms for samples previously limited due to vanishingly small amounts.

This assay was developed in collaboration between Illumina and Clontech and is sold and supported by Clontech. For ordering and additional product information, visit the Clontech product page.


Kits

Paired-end sample prep for library construction using cDNA from Clontech Kit:

For Cluster Generation and Sequencing using HiSeq 2000, HiSeq 1000,
or HiScanSQ (with cBot):

For Cluster Generation and Sequencing using Genome Analyzer IIx
(with cBot):

Protocols

Ultra Low Input mRNA-Seq Guide

Workflow

Smart-Seq Workflow