qPCR Plate Planner

Experiment metadata

Sample setup

Use "Name_Target_Condition". Group controls what’s analyzed together.

Color selection

Plate A — Assign samples/conditions to wells

Legend

Master Mix Planner

Target Assigned wells Extra wells Total wells used
Totals per target = per‑well × (Assigned + Extra).
Reagent µL per well
Totals per target
Total per well (µL)
Master tube total per target (µL)

Plate B — Enter Ct values

Paste a column or 2D block from Excel/Sheets starting at the focused cell.

Ct summary — All Groups

1. Calculation Mode
  • ΔCt: (Target - Reference). Raw expression.
  • 2^-ΔCt: Relative expression level.
  • ΔΔCt: (ΔCt Sample - ΔCt Control).
  • 2^-ΔΔCt: Fold Change (Relative to Control).
2. QC (Outliers)
  • Z-score: Best for triplicates. Removes wells > N standard deviations away from the mean.
  • IQR: Removes values outside 1.5x the Interquartile Range (box-plot method).
3. Error & Scale
  • SD / SEM: Standard Deviation (spread) vs. Standard Error (precision of mean).
  • Linear: Standard Y-axis (0, 1, 2...).
  • Log2: Symmetry for up/down regulation (-1, 0, 1...).
4. Statistics
  • t-test: Compares two groups (e.g., WT vs. KO). Measures if the difference between means is larger than random noise.
  • ANOVA: Compares 3+ groups. Prevents "false discoveries" that happen when running many t-tests on the same data.
  • BH (FDR): Essential for high-throughput (5+ genes) to correct p-values.
💡 Quick Tip: If your error bars are massive, tick QC (Z-score) and set Z to 1.5. This often cleans up technical noise from bad wells automatically.