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Source: GEO: Gene Expression Omnibus
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Total 772 results found since Jan 2013.
GSE158709 The effect of RNA polymerase V on 24-nt siRNA accumulation depends on DNA methylation contexts and histone modifications in rice
Contributors : Kezhi Zheng ; Dong-Lei YangSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Oryza sativaRNA-directed DNA methylation (RdDM) functions in de novo methylation in CG, CHG, and CHH contexts. Here, we performed map-based cloning of OsNRPE1, which encodes the largest subunit of Pol V, a key regulator of gene silencing and reproductive development in rice. We found that rice Pol V is required for CHH methylation on RdDM loci by transcribing long non-coding RNAs. Pol V influences the accumulation of 24-nt siRNAs in a locus-specific manner. Biosynthesis of 24-nt siRNAs on loci with high ...
Source: GEO: Gene Expression Omnibus - July 7, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Oryza sativa Source Type: research
GSE136193 Characterizing epigenetic effects of HISTONE DEACETYLASE 6 on DNA methylation, siRNA biogenesis and nucleosome positioning using two hda6 alleles in ros1 background
Contributors : Shoudong Zhang ; Huan Zhong ; Qianwen WangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaDNA cytosine methylation is a hallmark of epigenetic gene silencing. DNA demethylation requires ROS1, a bifunctional DNA glycosylase/lyases and open chromatin status mediated by IDM1. HDA6 is a RDP3-like histone deacetylase and was confirmed to mediate DNA methylation. In previous screening for ros1 suppressor, we identified two hda6 mutants revert...
Source: GEO: Gene Expression Omnibus - July 7, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Source Type: research
GSE173161 Comparative analysis of gene expression after Oct4 or Scrambled siRNA knockdown in HNSCC cell lines
Contributors : Anna Dubrovska ; Linda Hein ; Vasyl LukiyanchukSeries Type : Expression profiling by arrayOrganism : Homo sapiensBy employing a global gene expression profiling, we performed analysis of the molecular pathways which are deregulated in head-and-neck cancer cell lines FaDu, Cal33 and UTSCC5 after siRNA mediated knockdown of Oct4 comparing to Scrambled.
Source: GEO: Gene Expression Omnibus - July 1, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research
GSE154531 siRNA sequencing of Aedes aegypti from two regions of the Americas reveals insect-specific virus profiles with geographic structure
Contributors : Ken Olson ; Nelson Lau ; Adeline Williams ; Qicheng MaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Aedes aegyptiWe performed small RNA sequencing on recently colonized female Aedes aegypti from Mexico and Brazil. We compare small RNA profiles in midguts and abdomens (without ovaries) either non-bloodfed or 48 hours post non-infectious bloodmeal.
Source: GEO: Gene Expression Omnibus - July 1, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Aedes aegypti Source Type: research
GSE164125 BAF45D Cooperates with SMAD Signaling and Promotes Early Neural Differentiation in P19 Cells
Contributors : Hu Xiujuan ; Liu ChaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe sought to explore whether BAF45D regulates PAX6 expression through cooperating with TGF-beta/SMAD signaling in RA treated P19 cells. Here we identified BAF45D is required for expression of phosphorylated SMAD3 and PAX6 induced by RA. Genome-wide analysis revealed that during RA-induced early neural differentiation, BAF45D knockdown failed to activate TGF-beta/SMAD signaling and induce expression of Stat3 and Smad7, two negative regulators of TGF-beta/SMAD signaling. Moreover, BAF45D was immunoprecip...
Source: GEO: Gene Expression Omnibus - June 30, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE154232 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : OtherOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research
GSE154214 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partia...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research
GSE154148 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome b...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE178669 Next Generation Sequencing Facilitates Quantitative Analysis of Control siRNA, RAB11A siRNA1 and RAB11A siRNA2 suppressed EBC-1 cell's Transcriptomes
This study aims to find cellular pathway changes in RAB11A suppressed in lung squamous cell carcinoma cell line EBC-1 compared to control and to evaluate downregulating genes by RAB11A suppression by siRNA. Total RNA was extracted from EBC-1 transfected with control siRNA and RAB11A specific siRNAs using the RNeasy mini kit (Qiagen, Hilden, Germany). CAGE library preparation, sequencing, mapping, and gene expression and motif discovery analysis were performed by DNAFORM (Yokohama, Japan). In brief, RNA quality was assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0 and A260/280 and 260/2...
Source: GEO: Gene Expression Omnibus - June 23, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE162233 p38-MAPK mediated rRNA processing and translation regulation enables PrE differentiation during mouse blastocyst maturation
Contributors : Lenka Gahurova ; Pablo BoraSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusp38-MAPKs are stress activated kinases necessary for placental development and nutrient and oxygen transfer during murine post-implantation development. In preimplantation development, p38-MAPK activity is required for blastocyst formation. Additionally, we have previously reported its role in regulating specification of inner cell mass (ICM) towards primitive endoderm (PrE), although a comprehensive mechanistic understanding is currently limited. Adopting live embryo imaging, proteomic and trans...
Source: GEO: Gene Expression Omnibus - June 23, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE146047 HMGB1 as a rheostat of chromatin topology and RNA homeostasis on the path to senescence sCLIP
Contributors : Yulia Kargapolova ; Argyris PapantonisSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiensSpatial organization and gene expression of mammalian chromosomes are maintained and regulated in conjunction with cell cycle progression. This link is perturbed once cells enter senescence. The highly abundant HMGB1 protein, known to associate with bent and looped DNA, is actively depleted from senescent cell nuclei to act as an extracellular proinflammatory stimulus. Despite its physiological importance, we still lack understanding of the positioning and functional roles of H...
Source: GEO: Gene Expression Omnibus - June 23, 2021 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE164167 RNA-sequencing analysis of VEGFR2 knocking down in retinal pigment epithelial (RPE) cells upon glucose depletion.
Contributors : Bohan Xu ; Linbin Zhou ; Qishan Chen ; Jianing Zhang ; Lijuan Huang ; Shasha Wang ; Zhimin Ye ; Xiangrong Ren ; Yu Cai ; Weirong Chen ; Xuri Li ; Rong JuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-sequencing analysis was utilized to investigate the impact of VEGFR2 knockdown via siRNA on transcriptome profiling in primary human RPE cells under the glucose depletion condition compared to the control siRNA.
Source: GEO: Gene Expression Omnibus - June 16, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE115791 Transcriptome of primary and metastatic human melanoma with silenced STAT3
Contributors : Bozena Kaminska ; Dorota W Kulesza ; Kavita Ramji ; Jakub MieczkowskiSeries Type : Expression profiling by arrayOrganism : Homo sapiensPrimary and metastatic human melanoma cells were transfected with control siRNA or siSTAT3 to silence its expression. The global gene expression was evaluated after 48 h and related to gene levels in cells transfected with siRNA control.
Source: GEO: Gene Expression Omnibus - June 14, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research
GSE174612 Gene expression data from human breast cancer MCF-7 cells and its 4-hydroxytamoxifen-resistant derivative OHTR cells treated with an siRNA targeting TRIM47
Series Type : Expression profiling by arrayOrganism : Homo sapiensTo evaluate the effect of TRIM47 on NF- κB signaling in breast cancer cells, expression of TRIM47 was knocked down in MCF-7 cells and its 4-hydroxytamoxifen (OHT)-resistant derivative OHTR cells by small interfering RNA (siRNA). Microarray analysis was performed to analyze gene expression profiles of these cells.
Source: GEO: Gene Expression Omnibus - June 11, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research
GSE173837 RNA-seq and small RNA-seq in fission yeast CPF mutants that enable small-RNA-mediated epigenetic gene silencing
In this study, we have combined chemical mutagenesis with whole-genome sequencing in a sensitized S. pombe reporter strain to obtain a more comprehensive list of putative suppressors of small-RNA-mediated epigenetic gene silencing. This revealed more than 20 novel silencing-enabling mutations in genes that are associated with RNA processing, regulation of transcription, or post-translational protein modification. Focusing on factors involved in pre-mRNA cleavage and polyadenylation, we for example show that single amino acid substitutions in Yth1, which is responsible for polyadenylation signal recognition, lead to nearly ...
Source: GEO: Gene Expression Omnibus - June 7, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Schizosaccharomyces pombe Source Type: research
