LNA Technology for NGS and PCR Optimization

severe

Probe Integrity Compromised During Storage or Synthesis

Target RNA depletion efficiency is significantly reduced or absent. Sequencing shows minimal reduction in targeted reads despite proper protocol execution.

💡 3 · ✓ 4

severe

DNA Contamination Interferes with RNA Quantification and Depletion

RNA depletion shows poor efficiency with high residual target reads. RNA quantification may be inaccurate and inconsistent with expected values.

💡 3 · ✓ 4

severe

Improper Temperature Ramp During Probe Hybridization

Probe hybridization step was unsuccessful resulting in poor depletion. Target RNA removal is inconsistent or incomplete across replicate samples.

💡 4 · ✓ 5

moderate

Chemical Contaminants Inhibit Probe Hybridization

Depletion efficiency is reduced or completely absent. Target RNA remains at high levels after treatment despite using validated probe designs.

💡 4 · ✓ 5

moderate

Non-Uniform Depletion Across Targeted Sequences

Depletion efficiency varies significantly across different targeted sequences. Some target regions show good depletion while others remain at high levels.

💡 4 · ✓ 5

moderate

Genome Annotation Version Mismatch Between Design and Analysis

Target sequence used to design probes differs from the reference used to evaluate depletion. Depletion appears ineffective when analyzed against current genome annotations.

💡 4 · ✓ 5