H3K4me3 Marks in Normal and Cancerous Prostate Cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Aaron Statham
PROVIDER: E-GEOD-38682 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The histone modification H3K27me3 is representative of silenced regions of the genome. Changes between the normal and cancer state were investigated. Three PrEC samples, a normal cell line. Four LNCaP sample, a cancer cell line. Technical replicates.
2012-11-30 | E-GEOD-38683 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE38674: Genomic DNA in Normal and Cancerous Prostate Cells GSE38676: Expression Analysis of Normal and Cancerous Prostate Cells GSE38677: Mapping of Transcription Start Sites of Normal and Cancerous Prostate Cells GSE38682: H3K4me3 Marks in Normal and Cancerous Prostate Cells GSE38683: H3K27me3 Marks in Normal and Cancerous Prostate Cells GSE38684: Chromatin Looping of Normal and Cancerous Prostate Cells Refer to individual Series
2012-10-16 | E-GEOD-38685 | biostudies-arrayexpress
Project description:Mapping the locations of the DNA binding protein CTCF genome-wide to assess its colocalisation with expression domain boundaries. One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38684 | biostudies-arrayexpress
Project description:To investiagate copy number differences between PrEC and LNCaP cells, each was DNA sequenced. One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38674 | biostudies-arrayexpress
Project description:Capped analysis of gene expression (CAGE) sequencing was done on a normal and a cancer cell line to examine how promoter usage changes between these two states. One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38677 | biostudies-arrayexpress
Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear.<br><br>Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA.
2010-09-01 | E-MTAB-332 | biostudies-arrayexpress
Project description:Strand-specific RNA sequencing was done on a normal and a cancer cell line to examine how isoforms are used differently between these two states. One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38676 | biostudies-arrayexpress
Project description:We report the identification of LSD1 binding genomic regions in mouse embryonic stem cells (ESC) by high throughput sequencing. By obtaining over 10 million 36 bp reads of sequence from each chromatin immunoprecipitated DNA, we generated genome-wide maps for LSD1 and histone H3 dimethylated on lysine 4 (H3K4me2), the substrate for LSD1 in mouse ESCs. Our results showed an extensive overlap between the LSD1 and H3K4me2 genomic regions and a correlation between the genomic levels of LSD1/H3K4me2 and gene expression, including many highly expressed ESC genes. LSD1 is recruited to the chromatin of cells in the G1/S/G2 phases and is displaced from the chromatin of M phase cells, suggesting that LSD1 or H3K4me2 alternatively occupies LSD1 genomic regions during cell cycle progression. LSD1 knockdown by RNA interference or its displacement from the chromatin by anti-neoplastic agents caused an increase in the levels of a subset of LSD1 target genes. Taken together, these results suggest that cell-cycle dependent association and dissociation of LSD1 with chromatin mediates short-time scale gene expression changes during ES cell cycle progression. Examination of LSD1 and lysine 4 dimethylated histone H3 (H3K4me2) binding genomic regions in embryonic stem cells. Input genomic DNA and DNA immunoprecipitaed with control IgG was included as controls.
2012-10-03 | E-GEOD-18515 | biostudies-arrayexpress
Project description:Half of all human cancers lose p53 function by missense mutations, with an unknown fraction of these containing p53 in a self-aggregated, amyloid-like state. Here we show that a cell-penetrating peptide, ReACp53, designed to inhibit p53 amyloid formation, rescues p53 function in cancer cell lines and in organoids derived from high-grade serous ovarian carcinomas (HGSOC), an aggressive cancer characterized by ubiquitous p53 mutations. Rescued p53 behaves similarly to its wild-type counterpart in regulating target genes, reducing cell proliferation and increasing cell death. Intraperitoneal administration decreases tumor proliferation and shrinks xenografts in vivo. Our data show the effectiveness of targeting a specific aggregation defect of p53 and its potential applicability to HGSOCs. Vehicle vs. ReACp53 treatment in 4 different samples: 2 cell lines (MCF7 w/ WT p53 as negative control and OVCAR3 w/ R248Q p53) and 2 clinical specimens (primary cells from patient #8 w/ WT p53 as negative control and primary cells from patient #1 w/ R248Q p53)
2016-01-04 | E-GEOD-74550 | biostudies-arrayexpress
Project description:FoxA1 has been shown critical for prostate development and prostate-specific gene expression regulation. In addition to its well-established role as an AR pioneering factor,several studies have recently revealed significant AR binding events in prostate cancer cells with FoxA1 knockdown. Furthermore, the role of FoxA1 itself in prostate cancer has not been carefully examined. Thus, it is important to understand the role of FoxA1 in prostate cancer and how it interacts with AR signaling. To address these questions, we generated LNCaP cells with stable FoxA1 knockdown. We performed AR/FoxA1 ChIP-seq and microarray analysis of these cells. ChIP_Seq examination of AR and FoxA1 binding sites in LNCaP shCtrl and shFoxA1 cells
2014-06-02 | E-GEOD-37345 | biostudies-arrayexpress