Do you use the same ages, in my research the same result appeared and this is due to the difference in stages of differentiation .

See my research in this link :

https://www.researchgate.net/publication/282661476_Expression_Pattern_of_Stem_Cell_Markers_in_Developing_Mouse_Pancreas_Full_Text_PDF

Good Luck

Article Expression Pattern of Stem Cell Markers in Developing Mouse ...

 Thanks for your response Saleh Alkarim.

My question was not on how to perform H&E staining, it was more on to how to prepare the mice foodpad for histology without compromising on the kind of staining I want to perform with it. 

If you want to do HE or other histological stainings on the food pad, you can fix it in formalin 10 % and then process it normally (ethanol, xylen and paraffin) and then embed it in paraffin and cut it by microtome! 

Thanks for your response Javad. 

Isn't it necessary to decalcify the foot pad as they have bones? 

Indeed, in anatomy and histology foot pad contains fat and connective tissue. As I understand you want to work on paw. So decalcifcation is necessary after fixation:)

Anyway, if you want to investigate a special tissue which the bacteria affect on it (for example skin), I suggest to sample just your tissue (skin) for tissue processing (without bone). In this way decalcification is not necessary and your tissue will not damage by the mineral acids during decalcification.

My samples are mice footpad. I have attached a picture for your reference. After infection,  the footpad gets a little swollen. So we want to check the presence of bacteria as well as check cell infiltration by histology. (we also to FACs). 

We have never performed histology of this region in our lab. In literature I find few only fixing and few happened to fix and decalcify before making sections. 

If I have to decalcify? can you tell me how long and what is preferred to decalcify? 

Thanks for your response