BioMicroCenter:Sequencing Quality Control
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Why is QC Important?
It is very important to have a reliable measurement of the amount of starting material so that the sample can be prepared for hybridization and amplification on the flow cell. The ideal is a sample with 10nM of successfully ligated DNA. A 1.3ug/ul, 200bp sample is approximately 10nM.
Currently the optimum cluster range is from about 140,000 to 180,000. If a sample is too concentrated or the fragment sizes are too variable the GA will not be able to detect the reads properly. If the sample is too dilute the optimum number of reads per lane will not be achieved. Having reliable concentration measurements allows us to optimize the number of reads per lane and maximize the quality of data produced.
Possible Sample QC Techniques
- NanoDrop ND-1000- The NanoDrop is one of the most commonly used tools to measure the concentration of DNA in solution. The NanoDrop has a detection limit of about 5ng/ul. Unfortunately, due to noise at the lower detection limit, samples speced on the Nanodrop have not shown reliable results on the Solexa sequencer. We do not recommend using the NanoDrop as the primary method of determining concentration for samples on the Sequencer.
- 2100 BioAnalyzer - The Bioanalyzer produces data similar to that of gel electrophoresis, although it requires much less sample input (1uL) and provides quantification data in addition to valuable distribution information. Due to the amount of error introduced in low concentration or widely distributed samples the Bioanalyzer is not recommended as the primary method of determining concentration for samples that are less than 20ng/ul.
- Qubit - The Qubit is a selective flurometer that uses fluorescent dyes specific for dsDNA, RNA or protein to quantify samples. The Qubit is used in the Fraenkel lab to quantify their samples for Solexa sequencing. Information about this application can be found at: http://www.invitrogen.com/site/us/en/home/brands/Product-Brand/Qubit.html
- PicoGreen - PicoGreen is a fluorescent dye that binds specifically to dsDNA and allows for quantification. PicoGreen can be measured in a few different ways, the Boyer lab uses a photospectrometer and Invitrogen states that the Qubit can also be used. More information can be found at: http://probes.invitrogen.com/media/pis/mp07581.pdf
- RT-PCR, SYBERgreen assay - This assay uses primers that are specific for the adapters used during the ligation step of sample preparation. This allows for the amount of DNA that will actually bind to the flowcell to be quantified. The RT-PCR assay is recommended in addition to the techniques explained above and provides additional and more precise concentration information.
Flow Cell QC
SYBR Green Cluster Visualization- This protocol allows for the visualization of clusters on a flowcell after amplification and before it is put on the Genome Analyzer. It is especially helpful to ensure proper amplification has occurred if there has been a clog or an error on the cluster station or if an older Cluster Generation kit that may be expired is being used.
