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  • Cappable-seq Service now available !

    In close cooperation with New England Biolabs, Inc. (NEB), VERTIS is now able to make the new Cappable-seq method available to its customers. The method was developed by Laurence Ettwiller and Ira Schildkraut from NEB (Ettwiller, L. et al. 2016. BMC Genomics. 17, 1 (2016), 199).

    It represents the current most sensitive and robust method for the precise identification of bacterial transcription start sites (TSSs).

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WTSS FL-cDNA Normalization MicroRNA PARE DGE

Equalization of Gene Representation 

Expression of genes varies from a few to several thousand copies (mRNA molecules) in certain cell types. This high range of difference in gene representation makes it difficult to discover rare mRNAs even with the new ultra-high-throughput sequencing technologies, especially when using PacBio RS II  sequencing. To reduce high redundancy in cDNA populations, the representation of each sequence has to be equalized.

VERTIS offers a well-proven and highly efficient cDNA normalization using a kinetic denaturation-reassociation technique as outlined in the schema below. Already after one round of normalization nearly equal representation of each gene is achieved and a typical normalized cDNA library has a greater than 100-fold reduction in highly abundant clones, such as beta-actin. 

 

Normalized cDNA libraries are also very useful for sequencing with the Illumina MiSeq system. The MiSeq allows read lengths of up to 2x300 bp, but the data output is restricted to about 25 million reads per run. Therefore, the use of cDNA libraries with reduced redundancy can substantially increase sequence coverage per MiSeq sequencing run.

 

References

Wibberg, Daniel, et al. "Genome analysis of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB revealed high numbers in secreted proteins and cell wall degrading enzymes." BMC genomics 17.1 (2016): 1.

Pauli, Martina, et al. "De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite." BMC genomics 16.1 (2015): 1.

Lin, Ya-Fen, et al. "A comprehensive set of transcript sequences of the heavy metal hyperaccumulator Noccaea caerulescens." Front Plant Sci 5 (2014): 261.

 
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