FAQ (Frequently asked questions)
Genomic sequencing
What is Next Generation (Next-gen) sequencing?
The Next Generation sequencing technology makes it possible to sequence a complete genome within weeks, at a fraction of the costs of conventional (Sanger) sequencing technologies. This new sequencing technology has the power and flexibility to enable a wide range of genome-scale applications at the lowest cost per base.
Which next generation sequencing machine is used at Baseclear?
At Baseclear the Illumina Genome Analyzer II (Solexa sequencing) is used for NGS.
How much data is produced on the Illumina GAII?
There are several possibilities on our Illumina. A single lane with a 50 cycles run produces around 400-500 Mb of data, while a 50 cycle paired end-run produces around 850 Mb per lane. The maximum is at the moment 100 cycle paired-end run (so ~1600 Mb / lane). For more details, go to www.illumina.com.
How can I calculate the coverage?
You can easily calculate your coverage by dividing the amount of data through the length of the construct which is sequenced. For instance, a constuct of 20 Mb sequenced with a 50-cycle paired end run leads to a coverage of 850 Mb / 20 Mb = ~ 42,5 times.
How many lanes are on one flowcell?
Each flowcell consists of 8 lanes, however, one lane is used as internal control. On each flowcell therefore 7 lanes can be used for customer samples.
What are the possibilities of Next Generation sequencing at Baseclear?
We can perform genome sequencing, including resequencing (when a reference sequencing is known), and De Novo sequencing.
Also, we offer Transciptome sequencing (RNAseq or DGE) to determine the expression level of various genes. Our standard approach is to translate mRNA into cDNA, which is fragmented and subsequently sequenced.
Thirdly, we offer protein-DNA interaction analysis with our chIP-seq service. Chip-Seq combines chromatin-immunoprecipitation with Next-Gen sequencing technology to identify and quantify in vivo protein-DNA interaction on a genome-wide scale. The cost of this new technology is a factor 10 to 30 lower as compared to the conventional ChIP-microarrays.
How is the data delivered?
The data can be delivered either as raw data, or as aligned and assembled data. From the first of October, Walter Pirovano will strengthen Baseclear team as bioinformatician, focussing on the analysis of the NG sequencing data. For more information about these possibilities, please fill in our contact form (click here) or send an email to info@baseclear.com.
How much input material is needed?
The Illumina can work when using as little as 100 ng of starting material.
I have a question regarding NGS which is not answered in this FAQ, what should I do?
We will be happy to answer all your questions. Please fill in our contact form (button on the left top of the screen, or click here), or send an email to info@baseclear.com. We will answer your questions as soon as possible, but at least within 3 working days.
You can also call us at number +31 (0)71 523 3917.
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