Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA107507 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sall4 ChIP-chip in mouse ES cell line W4 using NimbleGen MM8 RefSeq Promoter array (2.5kb)
| PRJNA106613 | ENA
Project description:Increasing studies suggest that SALL4 may play vital roles in leukemogenesis. We have used chromatin immunoprecipitation followed by microarray hybridization as a screening tool to determine potential genes that may account for the role SALL4 plays in leukemogenesis. Analysis of SALL4 binding sites reveals that genes involved in cell death, cancer, DNA replication/repair, and cell cycle were highly enriched (p<0.05). These genes include 38 important apoptosis-inducing genes (TNF, TP53, PTEN, CARD9, CARD11, CYCS, LTA) and apoptosis-inhibiting genes (Bmi-1, BCL2, XIAP, DAD1, TEGT). Real-time PCR has shown that expression levels of these genes changed significantly after SALL4 knockdown, which ubiquitously led to cell apoptosis. Flow cytometry revealed that reduction of SALL4 expression in NB4 and other leukemia cell lines dramatically increased caspase-3, Annexin V, and DNA fragmentation activity. Bromodeoxyuridine-incorporation assays showed decreased numbers of S phase cells and increased numbers of G1- and G2- phase cells indicating reduced DNA synthesis, consistent with results from cell proliferation assays. In addition, NB4 cells that express low levels of SALL4 have significantly decreased tumorigenecity in immunodeficient mice. Our studies provide a foundation in the development of leukemia stem cell-specific therapy by targeting SALL4. Keywords: ChIP-chip The global targets of SALL4 were determined using a NimbleGen promoter tiling array (2.7kb, information below) in the human cell line NB4. Because SALL4 is thought to play a significant role in leukemogenesis we focused primarily on genes involved in apoptosis and only used the ChIP-chip array as a screening tool to identify potential genes that may bind these genes. Upon identification and verification of apoptosis genes bound by SALL4 we utilized functional assays to determine the effect of SALL4 on these genes. In addition, gene expression profiling was used to determine pathways functionally altered by Sall4 reduction. Source: UCSC Build: HG18 Probe Length: 50-75mer Median Probe Spacing: 100bp Probes per Array: 385,000 Feature Size: 16μm x 16μm Array Dimensions: 17.4mm x 13mm Overall Slide Dimensions: 1" x 3" (25 x 75mm) Recommended Storage: Store arrays desiccated at room temperature. Promoter tiling from 2200bp upstream and 500bp downstream of the transcription start site for RefSeq genes.
2008-05-17 | E-GEOD-10734 | biostudies-arrayexpress
Project description:BCL6 ChIP on chip using a Nimblegen custom tiling array
| PRJNA99725 | ENA
Project description:HOXA13 Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set
| PRJNA103921 | ENA
Project description:UTX Chromatin Immunoprecipitation on human HG18 Nimblegen 2 array promoter set
| PRJNA117163 | ENA
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
2010-07-08 | E-GEOD-22345 | biostudies-arrayexpress
Project description:H3K36me3 (ChIp-ChIp), H3K4me3 (ChIp-ChIp), H3K27me3 (ChIp-ChIp), 5mC (MIRA) and 5hmC (hMeDIP) profiles were analyzed in neural progenitor cells (NPC) and neurons by using Nimblegen Mouse ChIP-chip 2.1M Economy Whole-Genome Tiling - 4 Array Set. In order to compare two different techniques of 5hmC profiling, we performed 5hmC profiling with Hydroxymethyl Collector™ Kit (Active Motif) method and hybridized it on mouse Chr7 fragment (Nimblegen). As an independent experiment, 5hmC profiling was performed by using hMeDIP method and hybridized on mouse Chr7 fragment (Nimblegen). After MIRA enrichment and genome amplification, DNA was hybridized on mouse Chr7 fragment (Nimblegen).
2012-12-31 | GSE38118 | GEO
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
2005-05-27 | GSE2714 | GEO
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
2008-08-06 | GSE9289 | GEO