Project description:This SuperSeries is composed of the following subset Series: GSE22343: ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-H3K4me2, anti-LSD1 or anti-SUZ12 antibodies on HOX tiling array GSE22344: ChIP-chip of siGFP- or siHOTAIR-treated foreskin fibroblasts with anti-LSD1 or anti-SUZ12 antibodies on human HG18 Nimblegen promoter arrays Refer to individual Series
Project description:KYSE410 cells were treated with PBS, TNFα, IL1β, and LPS respectively and mRNA expression profiles were assayed by Nimblegen gene expression microarray human HG18 (12x135K) Investigation of the critical gene participating various inflammatory stimuli in the process of ESCC progression.
Project description:STAT1 ChIP-chip performed on Human Hela S3 Cells for three different platforms. Nimblegen ENCODE arrays which comprise 50mer oligonucleotides spaces every 38bps (overlapping by 12nts) (5 biological replicates), custom maskless array tiling most of ENCODE with 50mer oligonucleotides end-to-end (3 biological replicates) and custom maskless array tiling most of ENCODE with 36mer oligonucleotides end-to-end (2 biological replicates). The chromatin-immunoprecipitation protocol is the same for all samples, however the labelling and hybridization protocols differ between Nimblegen and custom maskless arrays. Keywords = Transcription Factor Binding, STAT1, ChIP-chip, Human, Genome Tiling Arrays Keywords: other
Project description:We used NimbleGen human CpG/promoter microarrays for profiling epigenetic changes (DNA methylation, H3K27me3 and H3K4me3 marks) in colon tumors (Duke's stage II) and matching mucosa samples from patients. Analysis of DNA methylation was done by using the methylated CpG island recovery assay (MIRA) technique with further hybridization versus input on NimbleGen human CpG/promoter microarrays. For profiling of H3K27me3 and H3K4me3 marks, we performed chromatin immunoprecipitation with H3K27me3 (#07-449, Millipore) and H3K4me3 (#39159, Active Motif) antibodies and further hybridized versus input on NimbleGen human CpG/promoter microarrays. All experiments were performed simultaneously for matching tissue samples.
Project description:The GeneChip® Human Promoter 1.0R Array is designed for chromatin immunoprecipitation (ChIP) experiments. Sequences used in the design of the Human Promoter array were selected from NCBI human genome assembly (Build 34). Repetitive elements were removed by RepeatMasker.
Project description:Mapping of in vivo targets for HSF2 by using mammalian tissue material in a global ChIP-chip promoter screen. Chromatin was isolated from three wild-type (WT) mouse testes, crosslinked and sonicated into fragments of 100-500 bp, and the quality of the DNA was controlled before the immunoprecipitation, showing no signs of degradation. The DNA amplified from the HSF2 immunoprecipitation samples was labeled and hybridized against the total input DNA samples, on a 1.5 kb promoter tiling array (NimbleGen Systems Inc.), covering ~26000 promoters of the mouse genome. After hybridization and scanning, HSF2 hybridization signals were Lowess normalized to produce log2 ratios (HSF2 ChIP/Input DNA) for all replicate arrays. The promoter values were calculated as average log2 ratios over all probes for each promoter. To identify the HSF2 target population, we used a non-arbitrary analysis method called RankProd described in Breitling et al. 2004. RankProd has been published as an R/Bioconductor package. Keywords: 1.5 kb mouse promoter ChIP-chip (MM5, NimbleGen Systems Inc.), mouse testis
Project description:Evaluation of four commercial high-resolution oligonucleotide microarray platforms, Affymetrix Genome-Wide Human SNP Array 6.0, Agilent Human Genome CGH 244A, Illumina HumanExon510s-duo and Nimblegen HG18 CGH 385k WG tiling v1.0, for genomic profiling of bone tumours.
