- Transcriptome analysis
- - RNA sequencing
- - Tag Profiling
- - Download sheet
Derek Butler
Derek is responsible for the Genome analysis services, which are based on next generation sequencing technology. Together with Erwin van Rijn he also handles the Gene to Protein services. In addition to this, he works on a number of collaborative research projects with universities and research institutes the objective of which is to develop novel and more efficient DNA-related services.
CALL +031 (0)71 523 3917
MAIL info@baseclear.nl
Transcriptome analysis
Our RNA-Seq services can assist in the determination of the expression of various genes. We can characterize all transcriptional activity, coding and non-coding, in any organism without a priori assumptions and achieve an unprecedented view of the transcriptome. Our standard protocol involves the translation of mRNA into cDNA, which is fragmented and subsequently sequenced. Analysis of the large quantity of sequencing data obtained renders the accurate comparison of expression levels possible.
mRNA-Seq service
Our mRNA-Seq service allows essentially unlimited discovery and profiling of the entire transcriptome. With no probes or primers to design, mRNA-Seq is free to deliver unbiased and unparalleled information about the transcriptome.
Tag Profiling service
For a slightly more directed search through genome-wide mRNA, we identify mRNA transcripts by their unique, positionally known 18 base cDNA tag. These tags can be mapped back to a reference genome thus allowing analysis of the expression of the expressed genes without prior knowledge of the genes of interest.
Small RNA discovery and Analysis service
Our Small RNA discovery and Analysis service allows the discovery of rare small RNA without previous sequence or secondary structure information in any organism. Via this service we can find novel small RNA, characterize mutations and analyse the differential expression of all small RNA in your sample simultaneously.
Approach
Our product specialist works out which combinations of transcriptome sequencing have to be performed. This will occur in close collaboration with the customer.
Starting material
Total RNA (5-10 ug)
Sequencing
- Single read or paired-end sequencing with the Illumina GAII
Bioinformatics
- Supply of the raw sequencing data (fasta or scarf)
- Optional: De novo assembly or alignment against the reference sequence, when available. The customer will get the contigs that are arranged from the alignment.
- Optional: Downstream options such as gene expression, cSNPs, novel transcripts, novel isoforms, alternative splice sites, allele specific expression and rare transcripts.
The bioinformatics strategy will be determined in close collaboration between the customer, our bioinformatics specialist and product specialist Genome Analysis..
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