User:Karmella Haynes/Notebook/Polycomb project/2010/10/29

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10/29/10

 * &#x2713; ChIP optimization: bind beads, wash, elute

ChIP co-IP optimization > Samples:
 * 1) KAH126-1 dx + α-H3K27me3 (07-449)
 * 2) KAH126-1 dx + α-rabbit IgG

> Make buffers:
 * 1) Complete Buffer III
 * 2) Low Salt Immune Complex Buffer
 * 3) High Salt Wash Buffer
 * 4) LiCl Immune Complex Wash Buffer

> Bind beads (Note: *H3K27me3 ab 07-449 was Protein A purified, Millipore)
 * Pellet Protein A* beads slurry, wash 3x with Complete Buffer III, and resuspend in original volume (store remainder at 4°C).
 * Bind protein-ab complexes with 10 μL beads; rotate at 4°C/ 2 hours

> Low Salt Immune Complex Buffer (LSIC) wash (2x, on ice) (Note: beads+complexes can be kept on ice for 1-2 hours)
 * Pellet beads at 3000 rpm/ 4 °C/ 2 min. Keep 100 μL supernatant "Sup" for Western, discard the rest.
 * Resuspend beads in 500 μL LSIC. Transfer to a fresh tube. Keep old tip inside original tube.
 * Incubate beads/LSIC on ice/ 5 min. (flick twice during incubation).
 * Pellet beads at 3000 rpm/ RT/ 30 sec. Keep 100 μL supernatant "W1" for Western, discard the rest.
 * With a fresh tip, add 500 μL LSIC to old tube w/ old tip. Use old tip to transfer LSIC to pellet (to collect up all remaining beads)
 * Repeat the previous wash and spin.

> High Salt Buffer (HSB) wash (2x, on ice)
 * Resuspend beads in 1 mL HSB.
 * Incubate beads/HSB on ice/ 5 min. (flick twice during incubation).
 * Pellet beads at 3000 rpm/ RT/ 30 sec. Keep 100 μL supernatant "W2" for Western, discard the rest.
 * Repeat wash and spin.

> LiCl Immune Complex Buffer (LICB) wash (1x on ice, 1x at RT)
 * Resuspend beads in 1 mL LICB.
 * Incubate beads/LICB on ice/ 5 min. (flick twice during incubation).
 * Pellet beads at 3000 rpm/ RT/ 30 sec. Keep 100 μL supernatant "W3" for Western, discard the rest.
 * Repeat wash and spin, but at room temp.

> TE buffer wash (2x, RT)
 * Resuspend beads in 1 mL TE pH 8.0.
 * Incubate beads/LSIC @ RT/ 5 min. (flick twice during incubation).
 * Pellet beads at 3000 rpm/ RT/ 30 sec. Keep 100 μL supernatant "W4" for Western, discard the rest.
 * Repeat wash and spin.

> Elute for Western
 * 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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