For yeast protocols from SGD, see here.

For DNA content analysis, see here.

For protein extracts (for immunoblotting), see here. 

For colony PCR of E.coli, see here.

For colony PCR of S. cerevisiae, see here.

For plasmid recovery from yeast cells, see here.

For APEX labeling, see here.

For IPs of V5-tagged proteins, see here.

For IPs of TAP-tagged proteins see here, as modified for mRBPs, followed by ddPCR.

For APEX-IPs for MS/MS, see here.