qPCR analysis for ChIP samples Cse4-3HA (a), Ste12-13Myc (b) and RNA polymerase PolII (c). For all qPCR analysis, normalization using the 2-ΔΔCp method was used to compare results from a given primer pair to a negative primer pair (respectively Cse4P2, Ste12P1 and Pol2P4) (Table 9). Error bars represent standard deviation across three biological replicates for relative enrichment to the negative primer pair. (a) Cse4p is enriched preferentially at the centromeres (Cse4P1 for CEN3 and Cse4P4 for CEN6) but not at two random non-centromeric locations (Cse4P2 and Cse4P3). (b) Ste12p binds known target sites in pseudohyphal growth. Ste12P1, Ste12P2, Ste12P3 and Ste12P4 represent respectively sites with no enrichment, low enrichment, medium enrichment and high enrichment as determined by ChIP-chip studies (Christopher M. Yellman, unpublished data). While the low enrichment site was not found to be significantly enriched for this ChIP sample, the medium and high enrichment sites were strongly present in our samples used for qPCR. (c) PolII primer pairs were selected using Steinmetz microarray data [54,64] to have three positive pairs (Pol2P1, Pol2P2 and Pol2P3) and one negative pair (Pol2P4). Positive targets were all significantly enriched over the negative control.
Lefrançois et al. BMC Genomics 2009 10:37 doi:10.1186/1471-2164-10-37