Allele specific RNA polymerase occupancy and gene expression analysis for 8 CEPH lymphoblastoid cell lines.

Allelic variation in gene expression is common in human genome. To understand genetic and epigenetic basis of allelic gene expression variation, we conducted allele specific RNA polymerase occupancy and allele specific gene expression analysis in CEPH lymphoblastoid cell lines. DNAs, RNAs and chromatin lysates were isolated at the same culturing condition across 8 cell lines. DNA analysis were performed following the standard Affymetrix SNP array protocol. RNAs were amplified using Affymetrix amplified double strand cDNA synthesis kit. DNAs from RNApolymerase ChIP were amplified using SIGMA WGA kit. Amplified cDNAs and ChIP DNAs were fragmented labelled and hybridized on Nsp/Sty arrays following the standard protocol.