I recommend Dynabead protein G from LifeTechnologies. It sounds like you have chosen protein G beads instead of protein A ones for a good reason. But if you are not sure which beads are the best for your antibody, then there is a good guideline on their website.

Protein G magnetic beads work quite well for me in ChIP-qPCR with either mouse or rabbit raised antibodies. I use Dynabeads from Invitrogen:

http://www.lifetechnologies.com/order/catalog/product/10003D

I recommend Dynabead protein G from LifeTechnologies. It sounds like you have chosen protein G beads instead of protein A ones for a good reason. But if you are not sure which beads are the best for your antibody, then there is a good guideline on their website.

Protein G Mag sepharose (GE Healthcare) is a good choice as the bead size is bigger than Dynabeads, the loss of beads while washings can be minimal. There by a better yield even its a low/bad ChIPer. also doesn't get dried up easily. Good luck   

Thank you all for the answers. I have tried GE and Millipore beads and GE gave better signal to noise ratio, although still not optimal. I will test the Dynabeads as the background is still too high with GE and MP.

Definitely try Dynabeads! They are the definite choice. Very low background compared to others I´ve tried. As Diu said, make sure to choose the right kind of G vs A. Alternatively do as we did in one lab I worked in, use a 50:50 mix of these in all ChIP experiments regardless of antibody.

Bad beads can really screw up your experiments and waste a lot of time. I cant remember the brand, but one kind I tested had background IPs 10-100 fold above the real IP I got with dynabeads and 100-1000 fold above the dynabead background....

Best of luck!

I also have a similar experience with beads that generated a high background signal over IPs. I think there is no best beads for everything. You just have to test and see what works for your sample (chromatin, cell line, etc.)

 Hi, Here is a few refs which might be of interest.

·          Curran et al 2009 Nature 459, 1079-1084 (25 June 2009) A soma-to-germline transformation in long-lived Caenorhabditis elegans mutants

·          Lim at al 2009 Nature 458, 529-533 (26 March 2009), “Chromatin remodelling factor Mll1 is essential for neurogenesis from postnatal neural stem cells”

·          Hammoud et al 2009 Nature 460, 473-478 (23 July 2009), “Distinctive chromatin in human sperm packages genes for embryo development”.

·          Khadaroo et al 2009 Nature Cell Biology 11, 980 - 987 (2009) The DNA damage response at eroded telomeres and tethering to the nuclear pore complex

·          Nielsen et al 2009 Nature Methods 6, 753 - 757 (2009), “A Flp-nick system to study repair of a single protein-bound nick in vivo”

·          Sorefan et al 2009 Nature 459, 583-586 (28 May 2009) A regulated auxin minimum is required for seed dispersal in Arabidopsis

·          Classen et al 2009 Nature Genetics 41, 1150 - 1155 (2009) A tumor suppressor activity of Drosophila Polycomb genes mediated by JAK-STAT signaling

·          Guan et al 2009 Nature 459, 55-60 (7 May 2009) HDAC2 negatively regulates memory formation and synaptic plasticity

·          Kolasinska-Zwierz et al 2009 Nature Genetics 41, 376 - 381 (2009) Differential chromatin marking of introns and expressed exons by H3K36me3

·          Pai et al 2009, Molecular Biology of the Cell  Vol. 20, Issue 4, 1213-1222, February 15, 2009, GINS Inactivation Phenotypes Reveal Two Pathways for Chromatin Association of Replicative and DNA Polymerases in Fission Yeast

·          Demetriades et al 2009, J. Virol. doi:10.1128/JVI.00097-09, The LMP1 promoter can be transactivated by NF- B directly

o    Wan et al 2009, MOLECULAR AND CELLULAR BIOLOGY, May 2009, p. 2346–2358, Role of the Histone Variant H2A.Z/Htz1p in TBP Recruitment, Chromatin Dynamics, and Regulated Expression of Oleate-Responsive Genes

o    Gkikopoulos et al 2009, Molecular and Cellular Biology, August 2009, p. 4057-4066, Vol. 29, No. 15, SWI/SNF and Asf1p Cooperate To Displace Histones during Induction of the Saccharomyces cerevisiae HO Promoter

o    Klopf et al 2009, Molecular and Cellular Biology, September 2009, p. 4994-5007, Vol. 29, No. 18, Cooperation between the INO80 Complex and Histone Chaperones Determines Adaptation of Stress Gene Transcription in the Yeast Saccharomyces cerevisiae,

o    Koinuma et al 2009, Molecular and Cellular Biology, January 2009, p. 172-186, Vol. 29, No. 1, Chromatin Immunoprecipitation on Microarray Analysis of Smad2/3 Binding Sites Reveals Roles of ETS1 and TFAP2A in Transforming Growth Factor β Signaling,

o    Liang et al 2009, MCB Accepts, published online ahead of print on 24 August 2009, Defective erythropoiesis in transgenic mice expressing dominant negative upstream stimulatory factor

o    Outwin et al 2009, Molecular and Cellular Biology, August 2009, p. 4363-4375, Vol. 29, No. 16, Smc5-Smc6-Dependent Removal of Cohesin from Mitotic Chromosomes,

o    Huang et al 2009, Molecular and Cellular Biology, August 2009, p. 4103-4115,

Vol. 29, No. 15, Differentiation-Dependent Interactions between RUNX-1 and FLI-1 during Megakaryocyte Development,

 kind regards

ketil

I want to thank you all for the answers, they helped me to finish crucial chip experiments that finally yielded a publication. :) Dynabeads was the choice, they gave minimal background.

http://nar.oxfordjournals.org/cgi/content/full/gkv371?ijkey=WdFf1Ch68lhSXwV&keytype=ref

NICE :)