What is Next Generation Sequencing?
The Next Generation Sequencing technology enables sequencing of an entire genome within matter of weeks, at a fraction costs when using Sanger Sequencing technology. This new technology is based on "sequencing by synthesis" and makes it possible to determine the sequence of the genome or transcriptome of any organism: with or without a reference sequence.
What Next Generation Sequencers does ServiceXS have?
ServiceXS offers services on the Illumina GAIIx and HiSeq. Next to that, we have access to the FL GX 454 and the new sequencing technology from Helicos: the HeliScope.
The Illumina GAIIx runs one flow cell at a time while the HiSeq is processes 2 flow cells at a time. One flowcell contains 8 lanes, sometimes one of the lanes is used for an internal control. For multiplexing (more than one sample per lane) possibilities or for consultancy, please contact ServiceXS.
What is the difference between Illumina sequencing and Helicos sequencing?
There are many similarities between Illumina sequencing (of which ServiceXS offers the GAII and HiSeq services) and True Single Molecule Sequencing (tSMS) of Helicos. The main differences in what you can do with or get as a result from the two approaches, are:
- Sample quality requirements: HeliScope can sequence archival and FFPE samples
- Sample quantity requirements: HeliScope can get results from a low amount of nucleic acids
- Sample prep: Because the HeliScope requires almost no sample prep and no amplification, the data is unbiased and direct measurements of your sample
- Error rate: Illumina has a lower error rate (wrongly mapped bases) compared to Helicos sequencing
- Illumina offers londer read lengths, paired-end module etc. that Helicos does not have
I want to sequence my sample: When should I choose the HeliScope and when the Illumina platform?
This is a complicated question and depends on your sample, your experimental set up, the application you are interested in and what scientific question you would like answered. Please contact ServiceXS for consultation.
What applications of Helicos Sequencing does ServiceXS offer?
ServiceXS is official service provider in DNA sequencing and we have validated this service successfully. Also our data analysis team is well equipped and skilled to handle the data sets generated with the HeliScope. We are validating the ChIP seq and RNA gene expression application as we speak. However, we cannot offer Direct RNA sequencing yet, due to the unavailability of the needed kits from Helicos.
Does ServiceXS also perform RNA or DNA isolation?
No. ServiceXS does not do RNA or DNA isolations, but we can advise you on isolation kits to use. We recommend the Macherey-Nagel RNA isolation kit. For customers in BeNeLux, ServiceXS recommends products supplied by BIOKÉ.
What is your policy concerning sample preparation for the Illumina sequencing?
ServiceXS can either do the sample preparation for you, or you can construct your own library. When you choose to do it yourself, please discuss this with your Project Manager at ServiceXS for an optimal Next Generation Sequencing (NGS) run.
Does ServiceXS take on projects that occupy less than one flow cell?
Yes, ServiceXS does not require the whole flow cell to be filled. A consequence of only several independent lanes is that ServiceXS has to wait for another project to fill up the flow cell in order to be cost effective. This can cause delay in performance of the experiments. Do note that eventhough you may share a flow cell with another customer, we keep all data confidential.
Do you offer bioinformatics for NGS and if so, to what extend is bioinformatics included in the project?
We can either deliver raw data or offer you bioinformatic services. Do not underestimate the complexity of data generated from NGS! If you do not use our data analysis services, please make sure your bioinfomaticians are familiar and experienced with the vast amount of data generated.