Yes, low quality and FFPE samples can be used with QuantSeq 3' mRNA-Seq FWD and REV kits.
The use of FFPE samples for QuantSeq-Pool is not recommended (please see this FAQ for more details).
| Table of Contents | ||||
|---|---|---|---|---|
|
...
When preparing libraries for comparative gene expression profiling, all libraries that will eventually be compared should be amplified using the same number of PCR cycles.
NOTE: The DV200 value is not a reliable predictor of the required number of PCR cycles needed.
If there are a range of optimal PCR cycle numbers predicted for your samples, you may wish to perform an additional endpoint PCR test to check the library yields are sufficient for sequencing. This is ideally done using half the library volume for a couple of samples that have different cycle number predictions (e.g., lowest, middle, and highest cycle number), and using the average number of cycles for the endpoint PCR (adding one additional cycle to account for using half the library volume). After purifying and quantifying these libraries, you can evaluate the relative yields and adjust the number of PCR cycles accordingly.
NOTE:Additional PCR and purification reagents provided in the PCR Add-on Kit for Illumina (Cat. No. 020.96) and the Purification Module with Magnetic Beads (Cat. No. 022.96) would be required for this type of endpoint PCR testing.