Why does the CytoScan Assay User Guide state on page 35 to always prepare Fragmentation Master Mix according to Table 9 even when processing less than 24 samples?
It is critical to have correct size of the fragments for an optimal hybridization. The fragmentation reagent is very viscous, and it is easier to get a correct proportion of enzyme when a larger volume is used. Therefore, our recommendation is to always prepare a master mix for 24 samples, even if a smaller number of samples are processed.
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What are the fill volumes of the reagents in the CytoScan Reagent Kit?
We can only guarantee the volume that is indicated on the label. Since our assurance guarantee is only provided for the label volume we advise not planning experiments or standard operating procedures based on potential overage volumes.
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What are the stopping points in the CytoScan Reagent Kit assay?
After any stage in the assay (except digestion), samples can be stored at -20 degrees C if one is not proceeding directly to the next step. However, once a stage has been initiated, it must be completed before storage of the samples.
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How many freeze/thaw cycles are validated for CytoScan Reagent Kit (24 samples)?
CytoScan Reagent Kit (Cat. No. 901808) is validated for for 4 in-use freeze/thaw events but have to use the kit within a month (30 days) once opened even if they have not gone through 4 freeze-thaws.
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What is the recommended genomic DNA extraction methods used for the CytoScan assay?
Both blood and cell line sample sources have been tested with the CytoScan assay.
Methods that include boiling or strong denaturants are not acceptable because the DNA would be rendered single-stranded. Genomic DNA extracted using the following methods have been tested at ThermoFisher Scientific:
QIAGEN - Gentra Puregene Kit
5 PRIME - PerfectPure DNA Blood Kit
The CytoScan assay requires genomic DNA concentration >50 ng/µL. Therefore, the elution volumes for each of the kits will need to be adjusted accordingly to achieve the desired concentration.
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