We stain for T-bet and other transcription factors quite often. What protocol are you using for your intracellular staining? We found staining much improved by using a FoxP3 staining kit. They're available from BD and eBiosciences
Hi, I totally agree with Michael! It makes such a big difference using the different specialized buffers: personally I prefer the eBiosciences "FoxP3" buffers...
I agree with the previous responses: using commercial kits can sign. improve the quality of transcritpion factor staining for FACS, e.g. the BD Fix/Perm buffer kits.
However, 3-4% T-bet+ cells might be not sooo low in first place ... depending on the condition were you get your cells from (organ, stimulated/primed in vivo?) this might actually be quite realistic.
Depending on the source of the cells, you could gate on a population which is known to express Tbet at higher level (NK cells) to check the quality of your staining. Running a PBMC sample may be helpful.
I did the same thing, i stimulated T cells for 48 hours and then detected the transcription factors. I had also about 5 % of T cells positive for T bet in controls unstimulated T cells, but with stimulation we found an increase (15 % of positive cells). The percentage of t cells positive for T bet in controls cells depend on the state of the patient (if he is a patient with chronic inflammation, then you can see an increase in T bet). To improve your staining, you can increase the incubation time (usually it is 30 min but you can try 45 min or 1 hour).