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qPCR ΔΔCt Analysis

Ct target/reference per sample → ΔCt, ΔΔCt and 2^-ΔΔCt fold changes with a group chart. The same math as the Excel workbook, live in your browser.

What this is for: Relative gene-expression quantification from target and reference Ct values, per sample and per group.

The formula: ΔCt = Ct(target) − Ct(reference); fold change = 2^(−ΔΔCt)

How to use:

  1. Enter one sample per line in the form: Sample, Group, Ct target, Ct reference.
  2. Label each sample's Group exactly 'Control' or 'Treated' — the Control label sets the reference mean ΔCt.
  3. Read the mean ΔCt of the Control group, then each sample's ΔCt, ΔΔCt and fold change in the per-sample results.
  4. Read the group summary — mean fold change with SD and SEM for Control and for Treated — and the fold-change chart.

qPCR ΔΔCt Analysis

Enter Ct of the target gene and of the reference (housekeeping) gene per sample, and label each sample's Group exactly 'Control' or 'Treated'. One sample per line: Sample, Group, Ct target, Ct reference. ΔCt = Ct target − Ct reference; ΔΔCt = ΔCt − mean ΔCt of controls; fold change = 2^−ΔΔCt.

Mean ΔCt of Control group
Control — mean fold change
Control — SD / SEM (n) / ()
Treated — mean fold change
Treated — SD / SEM (n) / ()
Prefer to work offline or keep a copy? The download link is right below.
Download the qPCR ΔΔCt Analysis workbook (.xlsx)
Notes & limits (from the workbook): Group labels must match 'Control' and 'Treated' exactly — the control group's mean ΔCt is the calibrator, exactly as the workbook's AVERAGEIF formula does. Fold changes are averaged arithmetically per group (the workbook's method), and SD/SEM are taken over those per-sample fold changes.