Question

explain why cathode rays are called negatively charged rays (in reference with Thomson's experiment)

Answer 1

According to J.J Thomson 's observation:

When electric field is applied on the cathode rays, they are deflected towards the positive plate of the electric field. This shows that cathode rays carry negative charge. Only negative charge species will attract to positive charge species.
Similarly, when a magnetic field is applied on the cathode rays, these rays are deflected in a direction which shows that they carry negative charge.