yeast chip seq - completely new to our lab!

[bombardior]

hi everyone, i will be attempting the first ever chip seq in our lab soon and i just have a bunch of questions that i can't find answers on and hoping someone with more experience could chime in.
this will be for yeast.
1. i've got my hands on a protocol that has me grow yeast in 50 ml to OD 0.7, then crosslink/formaldehyde and quench with glycine, per chip sample. does this seem about right?
2. for each pellet i collect from above, i actually want to chip with 2 different antibodies, so they'll be split in half. am i better of growing more cells or will that be enough DNA?
3. how can i ultimately test my 'efficiency'? or in other words, whether my chip worked? i know that after shearing, usually 1% is saved as an input. (and this is the step after which i plan on separating my 1 sample into 2 equal samples) then antibody is added to to pull down cross linked dna. after uncrosslinking and purification, can i just use qubit on the 1% and on the final purified stuff to see what my yield is like?
what is a typical yield in both ng and % of the input?
thanks a ton! i plan on using either miseq or hiseq with illumina.

[rnaeye]

If you are using antibodies used before in other publications, I would recommend you to read these articles. The same applies to specific protein you are trying to pull down. Amount of DNA you will pull down will vary a lot. For example, if you pull down one of the core histones, you will have no problem getting enough material to work on. If you are working a protein like Histone H1 (linker histone) in budding yeast, it will be more challenging since its abundance is much lower, so you will need more starting material. I hope this helps. There are tons of research and methods papers with yeast chip experiments.

[bombardior]

just thought i'd give an update.
i did the chip and got about 1.5 ng dna out. my 1% input was quantified at 50 ng. (something like 0.002% of total)
overall i'm pretty happy. this represents about 5% of the theoretical maximum i could obtain based on existing knowledge of binding site and their relative abundance with respect to the whole genome.

i will end repair, a tail, ligate adapter, pipin size select and report back