Protocol tips
Upstream tips |
Protocol tips |
Downstream tips |
|
-Avoid over fixation.
-purchase expensive, "hing end" sonicator to get reproducible shearing.
-Avoid repeated freeze/thaw cycles.
-Keep all reagents on ice when not in storage. |
|
Protocol tips |
-Avoid over fixation.
-purchase expensive, "hing end" sonicator to get reproducible shearing.
-Avoid repeated freeze/thaw cycles.
-Keep all reagents on ice when not in storage. |
Publication protocol
AsiSI-ER-U2OS cells (12) were treated with 300 nM 4-OHT (Sigma) for 4 h to induce AsiSI-ER nuclear localization and DSB generation by the AsiSI nuclease. FokI-U2OS reporter cells (13) expressing inducible ER-mCherry-LacI-FokI-DD were treated with 300 nM 4-OHT plus 1 μM Shield-I (Clontech) for 4 h to induce nuclear expression and stabilization of ER-mCherry-LacI-FokI-DD and DSB generation at the transgene-harboring Lac operator sequences by the FokI nuclease. Subsequently, ChIP was carried out using the EZ-ChIP Kit according to the manufacturer’s protocols (Millipore). The immunoprecipitated and input DNA were analyzed by quantitative PCR (qPCR) using the Rotor-Gene SYBR® Green PCR kit (Qiagen) on a Rotor-Gene Q system (Qiagen). The PCR conditions were an initial preincubation step at 95°C for 5 min followed by 45 cycles of 95°C for 5 s and 60°C for 30 s. The last amplification cycle was followed by a melting curve analysis to confirm the specificity of the PCR amplification. Relative IP values were calculated based on the threshold cycle (Ct) value using the 2−ΔΔCt method (16).
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