I am using Iba1 (WAKO) and CR3/43 (DAKO) antibody on paraffin embedded human brain sections. I cut two serial sections, which were exact replicates (same region of the brain) of each other.
On one section, I applied Iba1 antibody (slide a) and on the other replicate section, I applied CR3/43 antibody (slide b).
When I analyzed my staining under the microscope, I found increased CR3/43 staining whilst paucity of Iba1 staining was observed. Iba1 mainly stained ramified microglia (surveying microglia) but not many activated microglia (amoeboid shaped), whilst CR3/43 showed dense microglial activation. I thought that since Iba1 stains for resting & activated microglia, Iba1 and CR3/43 would compliment each other.
Can someone please guide me as to why this is the case? Is Iba1 a lysosomal marker and if it is, could be the reason as to why the activated microglia were not stained?
I would be more than grateful for your help.