contract.sol

pragma solidity ^0.4.0;

contract C {
    uint storedData;

    function set(uint x) public {
        storedData = x;
    }

    function get() public constant returns (uint) {
        return storedData;
    }
}

index.js

const Web3 = require('web3')

let web3 = new Web3(new Web3.providers.HttpProvider('http://localhost:8545'))

const abi = [{"constant":false,"inputs":[{"name":"x","type":"uint256"}],"name":"set","outputs":[],"payable":false,"stateMutability":"nonpayable","type":"function"},{"constant":true,"inputs":[],"name":"get","outputs":[{"name":"","type":"uint256"}],"payable":false,"stateMutability":"view","type":"function"}]

const bin = "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"

let contract = web3.eth.contract(abi)

let contractDeployed = contract.new({ from: web3.eth.coinbase, data: bin, gas: 2000000 }, (err, c) => {
  if (err) {
    console.error(err)
    return
  }
  if(!c.address) {
    return
  }

  console.log("address: " + c.address)

  let instance = contract.at(c.address)
  instance.set.call(10, (err, ok) => console.log('set', err, ok))
  instance.get.call((err, ok) => console.log('get', err, ok.toString())) /* (1) Here why 10 is not returned */
})

run.sh

yarn add web3@0.20.6
ganache-cli &
node ./main.js