Applications
Transcriptome Sequencing
Overview
New! GS FLX Titanium Series Transcriptome Sequencing
The Genome Sequencer FLX System offers the powerful combination of long sequencing reads (400 to 500 base pairs) and dedicated GS Assembler software, enabling the sequencing and assembly of transcriptomes. Perform straightforward cDNA sequencing to comprehensively analyze an organism's transcriptome, from small non-coding RNA to full-length coding messenger RNA (mRNA).
- Assemble ESTs de novo to discover the transcriptomes of uncharacterized and novel organisms
- Map ESTs to genome or transcriptome references for characterized organisms
- Perform genome annotation and expression analysis
- Study genetic variation including alternate gene splice isoforms, fusion transcripts and gene families
- Comprehensively compare transcriptomic differences between organisms/species, developmental stages, environmental conditions, and more
Open your transcriptome research to the millions of organisms without a reference sequence. Perform comprehensive de novo transcriptome sequencing of novel species as a new experimental method to easily analyze and annotate previously uncharacterized genomes. Coupling this approach with de novo genome assemblies is an effective method to confirm assembly accuracy and simultaneously annotate.
Benefit from Extra-Long Reads (400 to 500 bp)
- Long reads cover more exons and splice junctions, allowing more positive linkage of variants and longer extension into UTR regions.
- Long reads enable de novo transcript assembly.
- Long reads facilitate the use of fewer reads to characterize the genome, making data analysis faster and more cost effective.
- Long reads better enable the discovery of novel transcripts and isoforms by limiting the need to use reference data sets.
Use Innovative de novo Transcriptome Assembly Software
- Dedicated GS Assembler software is designed specifically for de novo assembly of transcripts, supporting the particular needs and conditions of transcriptome analysis.
- Easy-to-use GUI and command line user interfaces enable straightforward analysis for both biologists and bioinformatics users.
- Automatically align sequencing reads into isoforms ready for uploading into publicly available analysis software.
Figure 1: de novo Assembly of a Fungal Transcript: The GS FLX Titanium series long 400-500 bp EST reads (green) routinely span multiple exons - shown bridging up to 9 of the 19 exons in this example. The GS Assembler produced two full-length EST contigs (blue), revealing two full-length variants with alternative splicing occurring in the 5' UTR region. While no reference sequence was available for this newly sequenced species, the GenMark predicted gene is shown (red). Screenshot generated with Broad Institute's Argo Genome Browser.
Publications
- Zhao et al. Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line.. PNAS 106(6): 1886-91. (2009).
- Maher et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101. March 5, 2009.
- Sugarbaker et al. Transcriptome sequencing of malignant pleural mesothelioma tumors. PNAS 105: 3521-3526. March 4, 2008.
- Salehi-Ashtiani et al. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature Methods 5: 597-600. July 2008.
- Vera et al. Rapid transcriptome characterization for a non-model organism using 454 pyrosequencing. Molecular Ecology 17: 1636-47. April 2008.
Click here to see all Transcriptome Sequencing publications.