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OsJMJ705 preferentially activates stress-responsive genes

ABSTRACT: Histone methylation is important epigenomic information for gene regulation and genome activity To evaluate genome-wide effect of OsJMJ705 on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant. Gene ontology (GO) analysis revealed that up-regulated genes were significantly enriched for the categories of stress-responsive genes.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE48069 | GEO | 2013/12/10

SECONDARY ACCESSION(S): PRJNA208847

REPOSITORIES: GEO

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OsJMJ705 preferentially activates stress-responsive genes

Project description:Histone methylation is important epigenomic information for gene regulation and genome activity To evaluate genome-wide effect of OsJMJ705 on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant. Gene ontology (GO) analysis revealed that up-regulated genes were significantly enriched for the categories of stress-responsive genes. To evaluate genome-wide effect of OsJMJ705 on gene expression, we used the Affymetrix microarray technologies to analyze the transcriptomes of the wild type, over-expression plants and the T-DNA mutant 14 days after germination under normal growth conditions. Two biological repeats were performed. Gene expression changes between the samples were analyzed by AffylmGUI package from the R software.

2013-12-10 | E-GEOD-48069 | biostudies-arrayexpress

Hox-C9 activates the intrinsic pathway of apoptosis and is associated with spontaneous regression in neuroblastoma [cell line_genex_44k]

Project description:Single-color gene expression profiles from 2 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. To gain insights into the molecular processes occurring upon HOXC9 re-expression, we analyzed gene expression profiles of IMR-32 and SK-N-AS cells after Hox-C9 induction using microarrays. We used gene ontology (GO) annotations to find classes of genes that are significantly over-represented in gene sets that were either up- or downregulated after HOXC9 re-expression. One-color gene expression analysis Single-color gene expression profiles from 2 neuroblastoma cell lines were generated using 44K oligonucleotide microarrays. Total RNA of HOXC9- and GFP-expressing SK-N-AS and IMR-32 cells was isolated at 0, 6, 12, 24, 48 and 96 h using Trizol. To determine global differences in the expression profiles of HOXC9- and GFP-induced SK-N-AS and IMR-32 cells, mean expression levels of each gene between HOXC9-induced and control (GFP) cells were compared. Gene Ontology Tree Machine (GOTM) was used to identify functional categories associated with the condition of the respective cell line.

2013-03-28 | E-GEOD-45545 | biostudies-arrayexpress

Transcriptomic Assay of CD8 2012-05-15

Project description:In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naive individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.

2012-05-17 | E-MEXP-3635 | biostudies-arrayexpress

BID preferentially activates BAK while BIM preferentially activates BAX, affecting chemotherapy response.

Project description:Apoptosis is a highly regulated form of cell death that controls normal homeostasis as well as the antitumor activity of many chemotherapeutic agents. Commitment to death via the mitochondrial apoptotic pathway requires activation of the mitochondrial pore-forming proteins BAK or BAX. Activation can be effected by the activator BH3-only proteins BID or BIM, which have been considered to be functionally redundant in this role. Herein, we show that significant activation preferences exist between these proteins: BID preferentially activates BAK while BIM preferentially activates BAX. Furthermore, we find that cells lacking BAK are relatively resistant to agents that require BID activation for maximal induction of apoptosis, including topoisomerase inhibitors and TRAIL. Consequently, patients with tumors that harbor a loss of BAK1 exhibit an inferior response to topoisomerase inhibitor treatment in the clinic. Therefore, BID and BIM have nonoverlapping roles in the induction of apoptosis via BAK and BAX, affecting chemotherapy response.

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Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

Project description:We sought to determine H3K4me3 distribution in mouse embryonic stem (ES) cells deficient for RBP2 compared with wild-type cells. RBP2 modifies methylated lysine residues on histone tails. As a result of this analysis, we identified genomic regions with changed H3K4me3 status and described these in gene ontology (GO) categories.

2015-08-12 | GSE28348 | GEO

Changes in H3K4 methylation in KDM5A/JARID1A/RBP2 knockout cells.

2015-08-12 | E-GEOD-28348 | biostudies-arrayexpress

Caffeine-regulated transcripts in mouse hearts are p27-dependent

Project description:Overall question: How does caffeine administration for 10 days with the drinking water change the transcriptome of the heart? Are these changes dependent on the protein p27? Results: 242 of the 245 transcripts differentially regulated after caffeine administration in wildtype animals are p27 dependent, since they are not changed in p27-deficient littermates. Among the most highly enriched gene ontology (GO) categories for biological processes are GO-terms describing pathways, which take place in the mitochondria.

2017-11-30 | GSE100489 | GEO

Identification of the molecular basis of anti-cancer effect of Huaier.

Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None. Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes. For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..

| 2612481 | ecrin-mdr-crc

RNA_seq analysis on Tfh and Treg before and after abatacept treatment

Project description:Analysis of transcriptome data identified 96, 64 and 3 genes that were differentially expressed (DE, adj. P value < 0.05) following abatacept treatment in Tfh, Treg and CD4+CD45RO+PD1+CXCR5- T cells, respectively. We determined if abatacept treatment altered the core transcriptional profiles of Tfh and Treg lineages by comparing gene expression of bulk sorted Treg and Tfh cells from cryopreserved PBMCs at baseline, week 24, and after abatacept withdrawal. Analysis of differentially expressed (DE) genes in Tfh was performed using Gene Ontology (GO) term enrichment analysis. This analysis revealed 9 significantly enriched GO categories, which were related to processes involved in cell division and proliferation. DE genes in the enriched GO categories showed a highly significant correlation in Tfh and Treg cells, further highlighting the similarity in the response of these two populations to abatacept. In contrast to Tfh and Treg, acatacept had a minimal impact on CD4+CD45RO+PD1+CXCR5- T cells.

2018-12-27 | GSE121827 | GEO

Identification of reproduction-related genes in the hypothalamus of the sheep (Ovis aries) using the ONT full-length transcriptome sequencing technology

Project description:the hypothalamus tissues of high-reproduction small-tailed Han sheep and low-reproduction Wadi sheep were collected, and full-length transcriptome sequencing by Oxford Nanopore Technologies (ONT) was performed to explore the key functional genes associated with sheep fecundity. The differentially expressed genes (DEGs) were screened and enriched using DESeq2 software through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).

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