Most parts were purchased on eBay. The cost is very cheap, total is about 3000 yen (about 30USD).
Regarding the nice cube clear case, I bought it at Japanese 100 yen shop. Always I can find very cheap and useful parts for DIY there.

Parts List (price):

PH Electrode Probe BNC for Arduino: (JPY 690)
Liquid PH0-14 Value Detect Sensor Module: (JPY 809)
3 Pcs PH Buffer Solution Powder PH Test Meter Measure Calibration 4.00 6.86 9.18: (JPY 97)
1.8 Inch Mini Serial SPI TFT LCD Module Display with PCB Adapter ST7735B IC: (JPY 436)
USB Nano V3.0 ATmega328 16M 5V Micro-controller CH340G board For Arduino: (JPY 284)
Waterproof Digital Thermal Probe or Sensor DS18B20 Length: 1M: (JPY 139)
5/10Pcs Double-sided PCB Circuit Board Universal Prototype Strip Breadboard 7BC(JPY 384)
Cube clear case: (JPY 100)