Project description:We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes. Total RNA obtained from HeLa S3 cells.
Project description:We explored the relationship between the distribution of DNase I hypersensitive site(DHSs) and levels of gene expression. Expression values from 5 to 11 are raw log2 ratio-transformed data from gene expression arrays. We found that the distribution of DHSs in promoter region and CpG islands is positively correlated with gene expression levels and 3’UTR DHSs are negatively correlated with active expression of genes.
Project description:Treatment with the histone deacetylase inhibitor trichostatin a (TSA) changes the radial positioning of the CFTR gene in HeLa S3 cells. The gene relocates from the nuclear periphery to the nuclear interior. In Calu-3 cells the gene is located in the nuclear interior. To identifiy potential regulatory elements for the positioning of CFTR, the histone h3 and h4 acetylation patterns of untreated and TSA-treated HeLa S3 and untreated Calu-3 cells were determined by ChIP-chip. A CTCF site close to the CFTR promoter displayed consistent histone H3 hyperacetylation in TSA treated HeLa S3 cells and Calu-3 cells.
Project description:The goal of this study was to define how loss of full-length DEK reshapes global transcriptional programs in HeLa S3 cells by comparing gene-expression profiles of wild-type (WT) HeLa S3 and the 1E7 DEK-knockout cells generated by TALEN-mediated genomic disruption. The 1E7 clone lacks detectable full-length DEK, while retaining a low-abundance truncated DEK species, consistent with an alternative transcriptional start site/allelic expression.
Project description:We report the results of chromatin immunoprecipitation following by high-thoughput tag sequencing (ChIP-Seq) using the GA II platform from Illumina for the human transcription factor STAT1 in HeLa S3 cells. The STAT1 ChIP was performed using HeLa S3 cells that are stimulated using gamma-interferon. We have also generated a seqenced input DNA dataset for gamma-interferon stimulated HeLa S3 cells. Raw data for this study is available for download from the Short Read Archive database at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?study=SRP000703. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project description:BAF170 ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaced every 38bps (overlapping by 12nts). Goal is to identify binding sites for BAF170. Keywords = Transcription Factor Binding, BAF170, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip
Project description:FOS ChIP-chip performed on Human Hela S3 Cells for Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts). Goal was to identify FOS-binding sites. Keywords = Transcription Factor Binding, FOS, ChIP-chip, Human, Genome Tiling Arrays Keywords: ChIP-chip
