I use 12 volts usually from the battery,and because arduino has it's own regulator was never a problem.
This part is a little bit confusing. I think you meant to say putting 12V into the Arduino (either the barrel jack or Vin Pin) never had an issue because of the on-board regulator. However, in this case you put 12V into Analog In by mistake. Which has nothing to do with the regulator.
The Max input to any of the Arduino's inputs is ~5V. It is possible you destroyed the ATmega but it isn't likely. Usually you will just loose the I/O pin.
When trying to upload do any of the lights near the USB port flash at all? Maybe there was another mistake in your wiring that damaged the FT232 chip. Does it (or the Arduino) get warm/hot after being on for a few minutes?
If the FT232 is getting warm then it isn't the ATmega. If you can find one in stock or have another microprocessor handy, you can try swapping it out to see if communication resumes.
You might also try manually resetting the board just before uploading to see if the auto-reset is broken. (Search for your error message, there are about 6,000 pages on google that give this and other troubleshooting steps.)