reader.js

var reader = new FileReader();
reader.onload = function(e) {
  var bin = e.target.result;
  // bin is the binaryString
};
reader.readAsBinaryString(file);

upload.js

var xhr = new XMLHttpRequest();
xhr.open("POST", "upload.php");
xhr.overrideMimeType('text/plain; charset=x-user-defined-binary');
xhr.sendAsBinary(bin);