How do I normalize single-cell data? Should I use a normalization gene or the median/average Ct method?

Because the expression of every gene, including housekeeping genes, can vary 1,000-fold from cell to cell, normalizing by the traditional delta Ct value can be misleading.

We have found that normalization often does not impact single-cell data as significantly as in bulk cDNA experiments, so normalization is not always necessary. Normalizing by the median Ct reduces variability most reliably, and we recommend analyzing data with and without normalization to determine which method works best with each dataset.

For more information, see the Singular Analysis Toolset User Guide (PN 100-5066).


For Research Use Only. Not for use in diagnostic procedures.