We are implementing a grant related to the study of supertargets in secondary cultures of human neuroblastoma cells - IMR-32, Kelly, SH-SY5Y, SK-N-AS etc. Comparing gene expression between cell lines (using qPCR) under different conditions, the question arose - what should they be normalized to? So, in the standard calculation of ddCt, we set the value, for example, of the MYCN or TP53 gene to 1.0 (Control, intact). But this is not true, because in neuroblastomas the expression of this gene is significantly increased. As a result, the question remains: which line of which localization can we consider reference? Primary? Non-tumor? Tumorous, but not neurogenic (medulloblastoma, neuroblastoma)?
Thanks.
Are you not running any proper house-keeping/reference genes for normalization?
I have tried several possible housekeeping-type genes for SH-SY5Y in my study. Please find the primer information in the supplementary file: https://www.nature.com/articles/s41598-024-63005-y.
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