How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?
You can consider use of single-cell RT-qPCR kits such as this one if you have the budget for them. (Note: I have not personally used this kit, just putting out an idea)


  The Ambion® Single Cell-to-CT™ Kit contains a complete validated
  workflow for gene expression analysis for samples containing 1–10
  cells. Each kit contains reagents for sample preparation, reverse
  transcription, pre-amplification, and qPCR that have been optimized
  together in a simple workflow that can be completed in only 5 steps
  (see figure).