Next-Generation RNA Sequencing and Gene Regulation Analysis
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VERTIS is a privately owned research service company with a focus on RNA sequencing and gene regulation analysis. We provide our customers with access to the potential of revolutionary next-generation sequencing (NGS) technologies. Our innovative service is characterised by high quality, reliability and cost-efficiency.
VERTIS offers a complete product line, from project consulting, nucleic acid isolation, sample preparation and DNA sequencing to bioinformatic sequence analyses and data mining.
Our services cover the following areas.
Transcriptome analysis services
Our transcriptome analysis services include:
- RNA sequencing (RNA-seq), which discovers the entire universe of RNA, from small non-coding RNA (sncRNA, miRNA, piwiRNA, etc.) to full-length coding messenger RNA (mRNA)
- Digital gene expression, which measures the expression level of all genes in a given sample
- Cap analysis gene expression (CAGE) for genome-wide identification of transcription start sites (TSSs)
Analysis of complete epigenomes at single-base resolution
We can perform analysis of complete epigenomes at single-base resolution, including:
- Chromatin immunoprecipitation sequencing (ChiP-seq), which determines the sites of specific protein-DNA interactions that occur inside the nucleus (such as transcription factors or histone binding sites)
- DNA methylation analysis (Meth-seq) for obtaining a comprehensive and highly sensitive view of the methylation status of the chromatin
Next-generation sequencing (NGS) service
Because of its close co-operation with different partners, VERTIS has access to all popular NGS platforms. The Genome Sequencer (GS) FLX from Roche / 454 Life Sciences has one million reads per run and a read length of 400 bp, the Genome Analyzer from Illumina / Solexa has 80 million reads per run and a read length of 35, 75 or 100 bp, and the SOLiD from ABI has 160 million reads per run and a read length of 35 or 50 bp.
Millions of reads generated in a single experiment allow the transcriptomes and epigenetic modifications to be explored in a depth never seen before.
NGS rapidly creates enormous amounts of data. VERTIS supports its customers in extracting meaningful results from their experiments by applying state-of-the art bioinformatics, which covers:
- Quality trimming of raw sequence data
- Barcode filtering of reads
- De-novo assembly of reads
- Digital gene expression analysis
- Mapping of reads or contigs to reference genome
- BLAST analysis with contigs
- Identification of SNPs and DIPs (deletion / insertion polymorphisms)
- Extraction of biding sites and identification of conserved biding motives in ChiP-seq experiments
- Analysis of the methylation status of CpG islands
Classical custom cDNA library construction
In addition to its NGS-based services, VERTIS has long-standing experience in the construction of 'classical' cDNA libraries from all kinds of biological samples in a variety of formats (plasmid, phage, expression, etc.)
Digital gene expression
With respect to expression profiling, in comparison with microarrays, digital gene expression increases the dynamic range of analyses, has the ability to detect novel exons and does not have to deal with false positives.
We have developed techniques that allow high-quality and reliable synthesis of cDNA from the different RNA species (coding and non-coding RNA from eukaryotic and prokaryotic organisms) and from the whole range of tissues, organisms and environmental samples.
cDNA prepared by VERTIS is strictly strand-specific and therefore maintains the information about the strandedness of the transcripts. Our cDNA synthesis methods are perfectly adapted to the requirements of the new ultra-high-throughput sequencing technologies.
Special RNA-seq applications
Special applications for our RNA-seq services include:
- Whole transcriptome analysis: random-primed cDNA, enriched for sequences of the 5' and 3' ends of transcripts
- Normalisation of cDNA for ultra-deep sequencing and detection of very rare transcripts
- 5' and 3' tag cDNA for sequencing of 5' and 3' ends of the transcripts for CAGE-TSSs respectively DEG analyses
- miRNA sequencing: VERTIS was the first commercial provider to offer cloning and NGS analysis of microRNA (see Berezikov E et al. 2006, Diversity of microRNAs in human and chimpanzee brain. Nature Genetics 38:1375-1377)
- Bacterial transcriptomics: we are pioneers in the analysis of bacterial transcriptomes (see Sharma CM et al. 2010, The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464:250-255)
Advantages of VERTIS’s RNA sequencing and gene regulation analysis services
Our state-of-the-art RNA sequencing and gene regulation analysis technologies are based on competence gained from many years of pioneering research in the field of functional genomics, which translates as:
- Reliability, speed and cost-efficiency
- The highest quality guaranteed due to our strict and innovative quality management
- Customer-oriented flexibility
- Professional project management and support