Dataset features


Application: ChIP-on-chip analysis
Number of samples: 28
Release date: Jan 17 2007
Last update date: Mar 16 2012
Access: Public
Dataset link Identification of novel functional TBP-binding sites and general factor repertoires

Experimental Protocol

DNA fragments from ChIP with TBP antibodies and human U2OS cells were cloned, amplified and printed on glass slides to obtain TBP-binding sites microarray. ChIP has been performed with 28 antibodies against transcripton factors and histone marks, DNA from ChIP and input was amplified and hybridyzed on the TBP-binding sites microarray. The median ChIP/input ratios were normalized to median value of negative controls (myoglobin exons and promoter), averaged between 2 hybridizations and calculated as log2. For correlation analysis those targets with TBP ratio >2 were selected. Additionally, these targets were split to 2 datasets which contain targets overlapped and non-ovelapped with CpG islands (alignment and definition of UCSC genome browser).