CHIP
Reminder ­ Wear Gloves, lab coat and eye protection!!!
Day 1
1. Stimulate
or treat at least 1 x 106 cells on a 10cm dish. For LIF, treat at 50ng/mL to 100ng/mL
for 20 minutes as 37ºC.
2. Crosslink
histones by adding formaldehyde directly to culture medium for a final
concentration of 1%. For 10cm
plate with 10mL media, add 270uL of 37% formaldehyde.
3. Incubate
at room temperature for 20 minutes.
4. Take
off 7mL of media (leaving 3mL on the plate). Scrape cells in the 3mL and
transfer to a 15mL conical.
5. Pellet
cells for 4 minutes at 2000 rpm at 4ºC.
6. Aspirate
off media, add 5mL of ice cold 1x PBS. Resupend by vortexing. Pellet for 4 minutes at 2000 rpm at
4ºC.
7. Repeat
2 times.
8. Resuspend
pellet in 150uL of SDS lysis buffer supplemented with protease and phosphatase
inhibitors (PMSF, aprotinin, leupeptin, pepstatin, DTT, NaF, Na3VO4). Transfer lysate to eppendorf.
9. Incubate
on ice for 10 minutes.
10. Sonication
-
Tune sonicator before use.
-
Keep tip almost at bottom but not touching tube.
-
Keep on ice at all times ­ make a mound around tube to hold it
in place.
-
Sonicate 3 times on control setting 3 for 20 seconds each.
11. Centrifuge
samples for 10 minutes at 13,000 rpm and add 150uL of the sonicated cell
supernatant to a new 1.5mL microcentrifuge tube. Discard pellet.
12. Dilute the
sonicated cell supernatant by adding 1350uL CHIP dilution buffer supplemented
with aforementioned protease and phosphatase inhibitor (see step 8).
13. Remove 15uL
of the diluted supernatant to keep as your input fraction. Keep at 4ºC until ready to reverse
crosslinks.
14. Pre-clear
the 1.5mL of the diluted supernatant with 60uL of salmon sperm DNA/protein
Agarose 50% slurry for 30 minutes at 4ºC with rotation (use pipet tip with end
that has been cut off).
15. Pellet
agarose by spinning for 1 minute at 1000 rpm and then collect the supernatant fraction.
16. Add the
immunoprecipitating Ab. Incubate
overnight at 4ºC with rotation.
Day 2
17. Add 45uL of
the slurry and collect the Ab/histone complex by rotating at 4ºC for one hour.
18. Pellet
agarose for 1 minute at 1000 rpm at 4ºC. Carefully aspirate off non-specific
supernatant.
19. Wash by
rotating in homemade eppendorf tube rotator for 3-5 minutes with each of the
following buffers, spinning down after each with a 1 minute, 1000 rpm spin at
4¡C.
a. Lo
Salt wash (2 times)
b. Hi
Salt wash (2 times)
c. LiCl
wash (2 times)
d. 1
x TE (3 times)
Note: Keep buffers at 4ºC.
20. Freshly
prepare elution buffer (1% SDS and 0.1M NaHCO3).
21. Elute by
adding 200uL of elution buffer to the pelleted complex. Vortex briefly and mix occasionally for
15 minutes at room temperature.
22. Spin down
agarose at room temperature (1 minute), 1000 rpm) and transfer the supernatant
to a new collection tube. Repeat
elution to pelleted complex.
Combine the 2 eluates.
23. Add 16uL of
5M NaCl to the combined eluate (400uL), and 0.6uL 5M NaCl to the saved input
fractions.
24. Reverse
histone crosslinks by heating at 65ºC for 4 hours. (After this step, sample
can be stored at -20ºC.
25. To the
sample add 8uL of 0.5M EDTA, 16uL of 1M Tris-CL and 1.6uL of 10mg/mL Proteinase
K. To the input add 0.3uL of 0.5M
EDTA, 0.6uL of 1M Tris-HCL pH 6.5 and 0.6uL of a 10x dilution of 10mg/mL
proteinase K.
26. Incubate for
1 hour at 45ºC.
27. Bring up
volume of inputs with TE.
28. Extract DNA
once with 1 volume of phenol/chloroform.
Extract 2 times with ½ volume straight chloroform.
29. Add 10% 3M
NaOAc. Then add 2 volumes of 100%
EtOH. Add 1uL of stock glycogen.
30. Mix
vigorously and place at -80ºC for at least 1 hour.
31. Spin down at
max speed for 20 minutes.
32. Wash pellet
with 70% EtOH.
33. Resuspend in
10uL of TE.
34. Proceed to
PCR.
CHIP Solutions
SDS Lysis Buffer
1mL 10% SDS
200uL 0.5M EDTA
500uL 1M Tris HCl pH 8.0
8.3mL ddH20
Total Volume: 10mL
CHIP Dilution Buffer
50uL 10% SDS
0.55mL Triton-X 100
120uL 0.5M EDTA
835uL 1M Tris HCl pH 8.0
1.67mL 5M NaCl
46.8mL ddH20
Total Volume: 50mL
Lo Salt
0.5mL 10% SDS
0.5mL Triton-X 100
200uL 0.5 M EDTA
1mL 1M Tris-HCl pH 8.0
1.5mL 5M NaCl
46.3mL ddH20
Total Volume 50mL
Hi Salt
0.5mL 10% SDS
0.5mL Triton-X 100
200uL o.5M EDTA
1mL 1M Tris-HCl pH 8.0
5mL 5M NaCl
42.8mL ddH20
Total Volume: 50mL
LiCl
2.5mL 5M LiCl
0.5mL NP-40
0.5g Deoxychloric Acid
100uL 0.5M EDTA
0.5mL Tris-HCl
46.4mL ddH20
Total Volume: 50mL
1x TE pH8
1mL Tris-HCl
0.2mL 0.5M EDTA
98.8mL ddH20
Total Volume: 100mL