Have a look at this link: http://www.hoosiervalley.org/history/turkeys-and-trains/ Also check WikiPedia for poultry cars.
the NMRA MAGAZINE (formerly THE BULLETIN), May 2015, page 16 has an article on poultry cars. Some of these cars were still operating as late as 1956.
Live Poultry Transit Co. used the reporting marks LPTC
Poultry Transit Co used PTCX
Palace Poultry Car was another company who owned poultry cars. They used the PPKX reporting marks.
Pacific Wholesale Poultry Company Company of Petaluma CA owned at least two "chicken cars", #100 & #200. Reporting marks were PPWX.
Canadian Pacific, Canadian National, Southern, and possibly DL&W had poultry cars.
Here’s a good story with photo: http://condrenrails.com/FSVB/Engine-Terminals/Huber-KCS-2.htm
And most likely not all live poultry moved in poultry cars, but rather in conventional stock cars, and possibly even in ventilated boxcars. Since the industry's crates were more or less standardized they could be stacked pretty much anywhere in a car with ventilation that had some room.