I have a cell type that when it expressed the gene GATA3 they will fluoresce red. I have ran FACS and saw I had very good and clear positive and negative populations. When I ran qPCR looking at the gene expression of the GATA3 gene I see very low expression like 4 fold difference. why would this be? I have repeated the qPCR steps and changed primers but its the same low expression. Does anyone have any suggestions?
Protein function and transcriptional levels are not always well correlated. Transcription factors mRNAs are relatively low in abundance as they are tightly regulated in normal conditions. So even small fold-changes at the transcriptional level can lead to relatively large differences in the expression of downstream targets.
I'd suggest trying qPCR for a target of GATA3 to confirm your flow cytometry results.
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