ChIP-qPCR Percent Input

Back-calculate ChIP-qPCR percent input from Ct values and dilution.

Description

ChIP qPCR percent input uses a dilution-adjusted cycle difference under doubling-per-cycle assumptions.

ChIP qPCR percent input uses a dilution-adjusted cycle difference under doubling-per-cycle assumptions.^[1]

Back-calculate ChIP-qPCR percent input from Ct values and dilution.

When to use ChIP-qPCR Percent Input

Use this tool to back-calculate ChIP-qPCR percent input from Ct values and dilution.

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.

How to use ChIP-qPCR Percent Input and understand its results

Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
Enter inputCt, ipCt, inputDilutionFactor using the field table and calculation rules, then run the tool.
Read adjustedInputCt, percentInput, enrichmentFoldOverInput. The explanation below defines the units, signs, ordering and any flags or placeholder values.
If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.

Input field	Meaning	Value type; see rules below	Requirement
inputCt	Input sample Ct	number; minimum: 0	Required
ipCt	Immunoprecipitate Ct	number; minimum: 0	Required
inputDilutionFactor	Input dilution factor	number; minimum: 0	Required

Enter nonnegative Ct values and positive dilution; return adjusted Ct/fold/percent.

adjustedCt=inputCt−log2(dilution); percent=100×2^(adjustedCt−IPCt)

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
adjustedInputCt	Dilution-adjusted input Ct	number
percentInput	ChIP-qPCR percent input (%)	number; minimum: 0
enrichmentFoldOverInput	IP enrichment fold	number; minimum: 0

json

{
  "input": {
    "inputCt": 20,
    "ipCt": 18,
    "inputDilutionFactor": 4
  },
  "output": {
    "adjustedInputCt": 18,
    "percentInput": 100,
    "enrichmentFoldOverInput": 1
  }
}

Limitations and assumptions

Percent can exceed 100. No efficiency correction or primer specificity is supplied.

Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.

Alternative or Complementary methods

Use MeDIP Enrichment: Calculate MeDIP enrichment after volume normalization. For a complementary task, use HP1 Enrichment: Calculate HP1 enrichment after background correction.

References

ChIP-qPCR Percent Input — tool.io

Similar or alternative tools

MeDIP Enrichment
Calculate MeDIP enrichment after volume normalization.
HP1 Enrichment
Calculate HP1 enrichment after background correction.