Supplementary MaterialsAdditional file 1 Supplementary Table S1. not CP-673451 enzyme inhibitor detect histone H4 hyperacetylation in the myotube sample; pp_tube, fraction of pairs where both probes detected histone H4 hyperacetylation in the myotube sample. This data was used for the graphs in Figure ?Figure2A2A. 1471-2164-8-322-S1.pdf (18K) GUID:?0E2B4CAA-00BB-42D4-9A7C-6013AC08CE21 Additional file 2 Supplementary Table S2. Genomic correlation gene expression. For all pairs of Affymetrix DNA microarray HGU133A/B probesets detecting transcripts with transcription starts at a given distance range, the table shows the number of pairs according to their detection status. Columns are: distance, upper limit of distance range (in bp); total_blast, number of pairs at the distance range for the myoblast sample; aa_blast, CP-673451 enzyme inhibitor fraction of pairs where both probesets did not detect gene expression in the myoblast sample; pp_blast, fraction of pairs where both probesets detected gene expression in the myoblast sample; total_tube, number of pairs at the distance range for the myotube sample; aa_tube, fraction of pairs where both probesets did not detect gene expression in the myotube sample; pp_tube, fraction of pairs where both probes detected gene expression in the myotube sample. This data was used for the graphs in Figure ?Figure2B2B. 1471-2164-8-322-S2.pdf (18K) GUID:?08E50E18-EFE1-4BC4-94FD-9F66B5A77487 Additional file 3 Supplementary Table S3. Association between histone H4 hyperacetylation and gene expression in human myoblasts and myotubes. For all pairs of SNP-array gene and probes transcription starts at a given distance range, the table shows the real amount of pairs IL23R of SNP-array probes and DNA microarray probesets according with their recognition status. Columns are: range, top limit of range range (in bp); pT_blast, amount of pairs where in fact the SNP-array probe recognized histone H4 hyperacetylation as well as the DNA microarray probeset recognized gene manifestation in the myoblast sample; pS_blast, number of CP-673451 enzyme inhibitor pairs where the SNP-array probe detected histone H4 hyperacetylation and the DNA microarray probeset did not detect gene expression in the myoblast sample; aT_blast, number of pairs where the SNP-array probe did not detect histone H4 hyperacetylation and the DNA microarray probeset detected gene expression in the myoblast sample; aS_blast, number of pairs where the SNP-array probe did not detect histone H4 hyperacetylation and the DNA microarray probeset did not detect gene expression in the myoblast sample; pT_tube, number of pairs where the SNP-array probe detected histone H4 hyperacetylation and the DNA microarray probeset detected gene expression in the myotube sample; pS_tube, number of pairs where the SNP-array probe detected histone H4 hyperacetylation and the DNA microarray probeset did not detect gene expression in the myotube sample; aT_tube, number of pairs where the SNP-array probe did not detect histone H4 hyperacetylation and the DNA microarray probeset detected gene expression in the myotube sample; aS_tube, number of pairs where the SNP-array probe did not detect histone H4 hyperacetylation and the DNA microarray probeset did not detect gene expression in the myotube sample. This data was used for the graphs in Figure ?Figure33. 1471-2164-8-322-S3.pdf (19K) GUID:?2F501C41-18F2-44EB-8F64-0000FA78D2D5 Abstract Background SNP microarrays are designed to genotype Single Nucleotide Polymorphisms (SNPs). These microarrays report hybridization of DNA fragments and therefore can be used for the purpose of detecting genomic fragments. Results Here, we demonstrate that a SNP microarray can be effectively used in this way to perform chromatin immunoprecipitation (ChIP) on chip as an alternative to tiling microarrays. We illustrate this novel application by mapping whole genome histone H4 hyperacetylation in human myoblasts and myotubes. We detect clusters of hyperacetylated histone H4, often spanning across up to 300 kilobases of genomic sequence. Using complementary genome-wide analyses of gene expression by DNA microarray we demonstrate that these clusters of hyperacetylated histone H4 tend to be associated with expressed genes. Conclusion The use of a SNP array for a ChIP-on-chip application (ChIP on SNP-chip) will be of great value to laboratories whose interest is the determination of general rules regarding the relationship of specific chromatin modifications to transcriptional status throughout the genome and to examine the asymmetric modification of chromatin at heterozygous loci. Background Chromatin immunoprecipitation (ChIP) is a technique widely used to study interactions of proteins with specific genomic regions [1]. Several methodologies have been devised for the detection of the genomic fragments generated by a ChIP experiment (reviewed in [2]). In particular, the use of DNA microarray methodology (ChIP-on-chip) allows for high-throughput analysis of thousands of genomic sequences simultaneously [3]. Genome tiling arrays covering entire genomes [4] can be used to map the sites.