Hi,

I can suggest you 3-4 different ways:to use a gradient SDS gel before your transfer or you can use a filter with a cut off 100 kDa before you load your samples. 

1- use a gradient SDS gel for running your samples (4-12%)

2- Use 10 or 12% SDS resolving gel but run your electrophoresis very slowly (40 volts for 4 hour), wait until your 40 kDa protein left the gel. 

3- you can use a filter with a cut off 100 kDa before you load your samples (Millipore amicon ultra centrifugal filters)

4- You can design a specific primer set for your desired isoform's cDNA and first isolate total mRNA and convert  to cDNA, next amplify your cDNA with quantitative PCR to make sure your  isoform really expressed. (this is still indirect)

Good luck

Hello!

if you really want to show the different isoforms that are a bir far from each other I can recomend you to do a stripping, in case you can find a specific antibody for those isoforms

if you want to go ahead with that antibody, i suggest to Optimise the concentration of acrylamide in your gels. A low concentration is going to help your isoforms to resolve better, as they are quite big

rt pcr is always a boost to ensure your results are consistent at protein and genetic level 

Hello Mir

The PCR and Western blot results are indicated whether want to explain the transcrptional changes with protein changes in a determined time course or serial time course. Whether the gene is detected by PCR reaction (standard primer) although have many isoforms, you should detect the potein. According my exprience with Santa Cruz antibodies are a little special with the viability storage.

Have your antibody a long time store?

Do you store the antibody at -20ºC?

Do you try with other aliquot of antibody?

Regards

The reply of Dr. Cigdem Ozen is very satisfactory .