Probe-Based RT-qPCR Systems: RNA Input Quality from Blood & FFPE Extraction

In RT-PCR, a probe is a short, labeled oligonucleotide designed to bind a specific sequence within the amplified region. It carries a fluorescent reporter and a quencher. During amplification, the probe is degraded, separating the reporter from the quencher and generating a detectable fluorescent signal that correlates with target RNA abundance.

qPCR does not strictly require a probe — intercalating dye-based methods like SYBR Green can also be used. However, probe-based qPCR offers higher specificity, making it essential for clinical diagnostics, multiplex assays, and applications like BCR-ABL monitoring where discrimination between closely related sequences is critical. For RT-qPCR from blood or FFPE RNA, probes are strongly recommended.

FFPE-derived RNA is inherently fragmented due to formalin crosslinking. DV200 — the percentage of fragments >200 nucleotides — is the primary quality metric. A DV200 >70% is considered acceptable for most RT-qPCR and RNA-seq workflows. The Cambrian FFPE RNA Isolation Kit consistently achieves DV200 >70%, making it suitable for gene expression profiling and fusion detection.

The Cambrian Blood RNA Isolation Kit recovers an average of 2.17 µg from 0.5 mL, 5.64 µg from 1 mL, and 9.61 µg from 2 mL of whole blood. RNA yield scales linearly with input volume, and RIN values of 8.6–9.7 are consistently achieved, making it ideal for transcriptomics and high-sensitivity RT-qPCR workflows.

Yes. Both the Cambrian Blood RNA Isolation Kit and the FFPE RNA Isolation Kit include integrated or supplied RNase-free DNase treatment. This eliminates genomic DNA contamination, which is critical for accurate gene expression profiling and probe-based RT-qPCR where residual DNA can generate false-positive signals and compromise data integrity.

Yes. Both kits are designed for automation on the Manta platform by Cambrian Bioworks. The Blood RNA Kit features a 50-minute on-deck protocol (CBW-200-i4) with pre-filled, ready-to-use cartridges. The FFPE RNA Kit supports 96-well format automation. These formats are suitable for oncology labs, biobanks, and clinical diagnostic centers requiring scalable, reproducible nucleic acid extraction.