In which story did all the humans turn to clay?

There's no such story that tells "all humans turn to clay". I suppose what you mean is a story that says "humans came from clay". 

The story of the latter actually came from mostly different versions of mythology, the Bible, and Quran. 

According to the Greek mythology, Prometheus created men out of water and earth (water+earth(land)= mud/clay). 
According to Egyptian mythology, their God created humans from clay before putting them into their mother's womb. 
According to Hindu mythology, Parvati, the goddess of fertility, love, and devotion created Ganesh, the Lord of good fortune from clay and turned into flesh and blood. 

The most widely known verse of the Bible says, "the Lord formed man from the dust of the ground, and breathe into his nostrils the breath of life; then man became a living soul". (Genesis 2:7)
And the Muslim's Quran as well says the same thing.