Yeast Transcription Factor Chromatin Immunoprecipitation

Materials and Reagents

1. 500 ml of log-phase yeast cell culture per ChIP (at -0.9 x 10⁷ cells/ml, ~4.5 x 10⁹ cells per sample)
2. 37% formaldehyde
3. 2.5 M glycine in H₂O (heat sterilized)
4. Liquid nitrogen, dry ice/ethanol bath or -70 °C freezer
5. 0.5 mm Zirconia/Silica Beads (Bio Spec Products, catalog number: 11079105z )
6. Commercial protease inhibitor cocktails, for example:
   Roche Complete protease inhibitor cocktail tablets (F. Hoffmann-La Roche, catalog number: 11697498001 )
   Roche Complete Mini protease inhibitor cocktail tablets (F. Hoffmann-La Roche, catalog number: 11836153001 )
   
7. EZview anti-Myc affinity gel (red colored beads) (Sigma-Aldrich, catalog number: E6654 )
8. Minelute kit for final DNA purification (QIAGEN, catalog number: 28004 )
9. LiCl
10. NaOAc
11. Ethanol
12. Triton X-100
13. TE
14. NaCl
15. EDTA
16. Isopropanol
17. NP-40
18. Na-deoxycholate
19. SDS
20. Tris-buffered saline (TBS) (10x stock) (see Recipes)
21. Lysis/IP buffer (see Recipes)
22. Lysis buffer/500 mM NaCl (see Recipes)
23. IP wash solution (see Recipes)
24. TE/1% SDS (100 ml) (see Recipes)
25. TE/0.67% SDS (100 ml) (see Recipes)
26. TE (100 ml) (PH 8.0) (see Recipes)
27. 1 mM PMSF (Fluka, catalog number: 93482 ) (see Recipes)
    

Equipment

1. Millipore stericup sterile vacuum filter units, 500 ml funnel, 0.22 μm or 0.45 μm pore size (EMD Millipore, catalog number: SCGVU05RE , SCHVU11RE )
2. Syringe needle (BD Biosciences, catalog number: 305155 or 305156 )
3. 5 ml snap-cap tubes, polypropylene (preferred) or polystyrene (BD Biosciences, Falcon^®) 
4. 15 and 50 ml conical polypropylene screw-top tubes (BD Biosciences, Falcon^®)
   
5. Branson Sonifier 250 with microtip or Digital Sonifier S-450D (BD Biosciences)
6. Refrigerated tabletop centrifuges, e.g. Beckman GS-6R, GS-15R (Beckman Coulter), or Eppendorf refrigerated multipurpose centrifuges (Eppendorf^TM, model: 5810R and 5804R ) (or simply put an ordinary tabletop centrifuge in the cold room) 
7. Fume hood
8. FastPrep machine (FastPrep, catalog number: 6004500 )
9. Hemacytometer
   
10. Spectrophotometer
    

Procedure