Tuesday, December 4, 2007

Optimized ChIP Protocols

This page contains links to a chromatin immunoprecipitation protocol optimized with factorial and response surface methods.

The optimization resulted in two protocols that both have more than 10-fold higher throughput than the original. One of the protocols was optimized for speed and requires only 1.5 days to complete with a 46% average improvement in signal-to-noise ratio over the original protocol. The second protocol, optimized for signal-to-noise, requires 2.5 days to complete and achieves a 293% average improvement in signal-to-noise ratio over the original protocol. The optimizations were done in E. coli using three different transcription factors (two were primarily for validation).

Download the new ChIP Protocols (pdf)

Download the original ChIP Protocol (pdf)

The above links will always refer to the most recent version of the protocol if future improvements are added. If you have any questions or comments on the protocol, please post them to this blog.

All raw data and experiments that went towards this protocol optimization are in my Lab Notebook in the Chapter entitled: Towards a faster, more reliable ChIP protocol.

Older Versions

The protocol has a Change Log to describe what changes have occured between versions of the protocol. Archived older versions are below:

ChIP Protocol Version 1.2

ChIP Protocol Version 1.1

ChIP Protocol Version 1.0


Bill Hooker said...

Timing couldn't be better: a new postdoc recently joined our lab and is starting out on a ChIP project. I'll point her to your protocols. Muchas gracias!

J said...

Great! Best of luck and let me know if you all have any questions about things.