As the target gene dCT is negative, this is expressed higher than the housekeeping gene I use. Can I still use this data or do I need to re-run with a different housekeeping gene?
You're gene is highly expressrd, but nothing wrong with that. Did you expect otherwise? You can search online databased and atlased to see what is the exoressiin level of yiur gene in other/simillar cell typse compared to actin and see whether what you get in your pcr makes sense.