10/07/10
- ✓ ChIP qPCR: 126-1 and 132-8 samples
- ✓ ChIP optimization: second step (5-hour binding)
ChIP qPCR
> Optimization to make sure input gives low C(t) compared to no template ctrl.
> Set up each reaction in triplicate
> Templates (use 4.0 μL, 12 rxns each):
- KAH126-1 Input (#16), pos
- KAH126-1 αmyc IP (#18), unk
- KAH126-1 αIgG IP (#20), neg
- 0 template (dH2O)
- KAH132-8 Input (#16), pos
- KAH132-8 αmyc IP (#18), unk
- KAH132-8 αIgG IP (#20), neg
- 0 template (dH2O)
> Primers (24 rxns each):
- INKARF D
- INKARF E
- INKARF F
- GAPDH B
--> 750 nM primer mix = 30 μL 10 μM mix + 470 μL H2O
Reagent |
1 rxn |
Primer mix (x25)
|
ChIP DNA (1:1) |
4.5 |
---
|
SYBR Green mix |
7.5 |
187.5
|
750 nM primers |
3.0 |
75.0
|
dH2O |
--- |
---
|
|
15.0
|
--> Aliquot 31.5 primer mix into 1st well of each triplicate set
--> Add 13.5 DNA to primer mix
--> Aliquot 15.0 rxn mix to other 2 wells in 3x set
Bio-Rad CFX96 qPCR (Kirschner lab)
--> Use Bio-Rad 96-well low profile plate MLL-9601 + Microseal "B" film
- 95°C/ 5 min.
- [95°C/ 15 sec, 57°C/ 15 sec, 72°C/ 15 sec] x45
- Melt curve range 57°C -> 95°C/ 0.5°C per step
ChIP optimization
> Continued from yesterday
> Make enough complete sonication buffer for bead-ab wash and washes for elution (12 mL)
> Chromatin + antibody samples (1,2)
--> Add 10 μL prepped Protein A Sepharose beads
--> Rotate at 4°C/ 5 hours
> Beads + antibody samples
--> Wash off unbound antibody: pellet beads (3000 rpm/ 4°C/ 3 min.), discard sup, wash w/ complete sonication buffer (keep on ice); repeat 2x
--> Resuspend in 250 μL complete sonication buffer + 250 μL chromatin (KAH126-1 dx)
--> Rotate at 4°C/ 5 hours
> Wash and elute
--> Same protocol as αmyc-bead conjugate IP, but gently wash 3x instead of 4x
--> Elute with 60 μL 1x loading dye + 50 mM DDT (enough to load two Western wells)
--> Heat at 65°C/ 10 min., vortex every 2 min.
--> Pellet beads, transfer supernatant to new tube
--> Heat supernatant at 100°C/ 5 min.
--> Store at -20°C until Western blot.
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