H3K27me3 Marks in Normal and Cancerous Prostate Cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE38683 | GEO | 2012/11/30
SECONDARY ACCESSION(S): PRJNA168464
REPOSITORIES: GEO
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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:H3K4me3 ChIP-seq was done to examine transcription start sites in a genome wide manner, and compare results to CAGE-seq
2012-11-30 | GSE38682 | GEO
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:H3K4me3 ChIP-seq was done to examine transcription start sites in a genome wide manner, and compare results to CAGE-seq One PrEC sample, a normal cell line. One LNCaP sample, a cancer cell line.
2012-11-30 | E-GEOD-38682 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2012-10-16 | GSE38685 | GEO
Project description:Few quantifiable tissue biomarkers for the diagnosis and prognosis of prostate cancer exist. Using an unbiased, quantitative approach, this study evaluates the potential of three proteins of the 40S ribosomal protein complex as putative biomarkers of malignancy in prostate cancer. Prostate tissue arrays, constructed from 82 patient samples (245 tissue cores, stage pT3a or pT3b), were stained for antibodies against three ribosomal proteins, RPS19, RPS21 and RPS24. Semi-automated Ox-DAB signal quantification using ImageJ software revealed a significant change in expression of RPS19, RPS21 and RPS24 in malignant vs non-malignant tissue (p<0.0001). Receiver operating characteristics curves were calculated to evaluate the potential of each protein as a biomarker of malignancy in prostate cancer. Positive likelihood ratios for RPS19, RPS21 and RPS24 were calculated as 2.99, 4.21, and 2.56 respectively, indicating that the overexpression of the protein is correlated with the presence of disease. Triple-labelled, quantitative, immunofluorescence (with RPS19, RPS21 and RPS24) showed significant changes (p<0.01) in the global intersection coefficient, a measure of how often two fluorophore signals intersect, for RPS19 and RPS24 only. No change was observed in the co-localization of any other permutations of the three proteins. Our results show that RPS19, RPS21 or RPS24 are upregulated in malignant tissue and may serve as putative biomarkers for prostate cancer.
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Project description:Examination of H3K27me3 histone modification in A549 cell line H3K27me3 ChiP-Seq
2015-12-11 | E-GEOD-75903 | biostudies-arrayexpress
Project description:H3K27me3 is a chromatin modification depositied by Suz12, a component of the Polycomb Group 2 complex, and is associated with transcriptional repression. In contrast, H3K79me2 is a chromatin modification associated with active gene transcription. It is deposited by the histone methyltransferase Dot1L and generally is localized just downstream of the transcriptional start site and extends down the body of the gene. To gain insight into the transcriptional state of genes in hES cells, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide occupancy of the H3K27me3 and H3K79me2 chromatin modifications and genome-wide occupancy of the Suz12. DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing A sample of whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against H3K27me3, H3K79me2, and Suz12 (Abcam).
2010-10-01 | E-GEOD-24463 | biostudies-arrayexpress
Project description:Background: Nucleosome organization within chromatin can be altered through the incorporation of histone modifications that in turn affects gene expression. Accordingly, the Polycomb Group (PcG) complexes PRC1 and PRC2 through the incorporation of H2AK121ub and H3K27me3 marks, respectively, maintain the repression of target genes; however, little is known about the exact function of these modifications in shaping nucleosome array at target genes, especially in plants. Results: By using two different MNase-seq datasets we analyzed the nucleosome occupancy profile of different PcG target genes in Arabidopsis. We found that PcG targets strongly differ in their nucleosome organization depending on the marks that they carry. Our data indicate that H2AK121ub marks play a role in fine-tuning +1 nucleosome position, while H3K27me3 marks impact nucleosome spacing and chromatin accessibility at both promoter and gene regions. Furthermore, analyzing the nucleosome profile of transcriptionally active PcG target genes in WT seedlings we found that their apparent activated state may be actually due to transcriptional heterogeneity across different cells. Conclusion: Our findings show that H2AK121ub and H3K27me3 marks differentially affect nucleosome organization in Arabidopsis, displaying additive effects when co-localizing at target genes.
2022-02-02 | GSE135978 | GEO
Project description:H3K27me3 is a chromatin modification depositied by Suz12, a component of the Polycomb Group 2 complex, and is associated with transcriptional repression. In contrast, H3K79me2 is a chromatin modification associated with active gene transcription. It is deposited by the histone methyltransferase Dot1L and generally is localized just downstream of the transcriptional start site and extends down the body of the gene. To gain insight into the transcriptional state of genes in hES cells, chromatin immunoprecipitation coupled with massive parallel sequencing (ChIP-seq) was performed to determine the genome-wide occupancy of the H3K27me3 and H3K79me2 chromatin modifications and genome-wide occupancy of the Suz12.
2010-10-01 | GSE24463 | GEO