Beta-Actin good RT-PCR Control?

[Richard R. Hardy]

In article <3e1ioo$1nn at netnews.upenn.edu>, smoore at mail1.sas.upenn.edu
(Sean David Moore) wrote:

> Dear BioNetters....
>         Here's a situation for you.  I have been isolating human alveolar 
> macrophages from sick patients.  I treat them with different experimental 
> proteins and later look for message of cytokines.  I have lately had 
> trouble finding beta-Actin as a positive RT-PCR control..I think there 
> may be two problems:
> 
> 1)  We are using total RNA for the RT, not mRNA ( not enough sample )..
> this may drown out the Actin message during Random primed RT...so I 
> switched to Oligo-dT...I still worry about using too little actual mRNA 
> in the RT.
> 
> 2)  Also, these macrophages have benn settled for at least 24 hours 
> before treatment.  Their beta-Actin production may be at low levels to 
> start with and treating them with something like LPS could severely 
> reduce Actin message...I may be looking for the wrong positive control...
> 

We routinely use b-actin with cDNA made from total RNA isolated from
10^4-10^5 cells and it usually gives a nice EtBr band after 18-20 cycles
(using 1/5 of the cDNA).  This includes resting B cells.  We get good RNA
using GITC/CsCl method (the "everybody does it" technique).  Recently
we've found that the "TRI-Reagent" (quick prep, no CsCl spin) also gives
good EtBr b-actin signal (at 35 cycles) from as few as 10 cells (!).  So I
think it's a good positive control and total RNA should be OK; we do,
however, use random hexamers, not oligo-T.  Perhaps your RNA is being
degraded by the macs?

-- 
R. Hardy
Member, Institute for Cancer Research,
Fox Chase Cancer Center, Philadelphia, PA
(215) 728-2463