When you observe fluorescence in cells after knocking in a target gene using a gene editing method (such as CRISPR-Cas9) but are unable to detect the target band in subsequent PCR analysis, there could be several reasons for this discrepancy.

• The gene editing process might have caused unintended mutations at off-target sites. While the cells may show fluorescence due to the successful integration of the gene at the target site, off-target effects can interfere with the correct amplification of the target gene in PCR.
• Depending on the size of the inserted sequence, it's possible that the PCR primers you're using might not be suitable for amplifying the target band efficiently.
• Incorrect primer design can lead to amplification failure.
• If the gene integration occurred at a low copy number, it might not be detected by PCR using conventional methods.

@Barış Eran's,If the gene integration occurred at a low copy number,what method should be used to detect it?

Kang Zong In such cases, you may using more sensitive techniques to detect low-copy gene integrations. qPCR, Amplification by Transcription, Next-Generation Sequencing, nested pcr are some methods you could consider.