GSE194186 Arabidopsis LSM1 and DCP5 proteins aid evasion of translational repression during Cauliflower Mosaic Virus infection
Contributors : Hoffmann Gesa ; Mahboubi Amir ; Bente Heinrich ; Garcia Damien ; Hanson Johannes ; Hafr én AndersSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Arabidopsis thalianaProcessing bodies are tightly connected with the RNA silencing machinery. Deletion of processing body components leads to succeptibility of Cauliflower Mosaic Virus to translational repression. Here, we investigated if this succeptibility is mediated through differential sRNA targeting of the viral genome. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE125556 Differential expression of LncRNAs and mRNAs and their modulated network construction during the process of HIV transcription
Conclusion: Quantitative detection results of cellular levels of total HIV DNA and RNA can distinguish whether HIV is in the state of active transcription. During process of HIV transcription, the differentially expressed LncRNAs involve the biological process of gene expression regulation, the hub genes excavated form the modulated network may become the potential candidate targets for HIV antiviral treatment. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE125755 Copper regulation of HIF-1 transcriptional activities
Contributors : Wenjing Zhang ; Pengfei HanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Macaca mulattaHIF-1 regulated VEGF expression were upregulated in reponse to ischemic injury. However, the VEGF mRNA level were increased in the early stage but decreased in the late stage of myocardial infarction. We found that activities of HIF-1 binding to the HRE sites were possiblely responsible for the differential expression of VEGF. The HIF-1 binding activities were regulated by copper. After ischemic injury, copper concentrations were decreased in the infarct myocardium in the late sta...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Macaca mulatta Source Type: research

GSE126005 Deep sequencing reveals an acute inflammatory signature in chronic Peyronie ’s disease
Conclusions: Our analysis suggests that, even in an established, chronic PD-plaque, acute inflammatory pathways are still active. We show for the first time that TNF α and TLR-activation could be an important pathway in PD-pathophysiology. Additionally, we suggest that this process is potentially maintained through macrophages. Release of TNFα induce chemoattraction of more macrophages by CCL2 production of (myo)fibroblasts. Both could lead to development of novel druggable targets and more representative disease models. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE144650 mTEClo/int RNAseq profiling in three mouse models of impaired mTEC/Tcell crosstalk
Contributors : Magali Irla ; Matthieu GiraudSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusmTEC/Tcell crosstalk drives transcriptional and epigenetic programs conditioning immunological tolerance (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE144680 Chromatin state of mTEClo/int in the RipmOVAxOTII mTEC/Tcell crosstalk mouse model
Contributors : Magali Irla ; Matthieu GiraudSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusmTEC/Tcell crosstalk drives epigenetic programs conditioning immunological tolerance (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE145995 Genome-wide transcriptional profiling of C. elegans in a heavy metal contaminated soil after nZVI treatment
Contributors : Carmen Fajardo ; Margarita Mart ín ; Mar Nande ; Pedro Botías ; Jesús García-Cantalejo ; Gerardo Mengs ; Gonzalo CostaSeries Type : Expression profiling by arrayOrganism : Caenorhabditis elegansClassical ecotoxicological test and high-throughput molecular tools (microarray) were conducted on C. elegans to assess the effectiveness and ecosafety of a nanoremediation strategy applied to a highly polluted soil environment with heavy metals (HMs). We stablished a profiled gene expression in C. elegans exposed to the polluted soil, treated and untreated with nZVI. The results obtained s...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by array Caenorhabditis elegans Source Type: research

GSE153265 The imprinted Zdbf2 gene finely tunes hypothalamic control of feeding and growth in neonates.
Contributors : Juliane Glaser ; Julian Iranzo ; Deborah Bourc'hisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo allow identification of differentially expressed genes between WT and Zdbf2-KO hypothalamus in mouse pups at 3 and 10dpp, mutants and control RNA-seq were conducted starting from whole hypothalamus RNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE156553 TGF β1 promotes collective invasion of oncogenically transformed intestinal organoids by inducing partial epithelial-mesenchymal transition independently of Snail1 and Zeb1
Contributors : Marion Flum ; Severin Dicks ; Monika Schrempp ; Alexander Nystr öm ; Melanie Boerries ; Andreas Hecht ; Yu-Hsiang TengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCancer cells simultaneously featuring epithelial and mesenchymal traits appear particularly competent to invade and metastasize. However, genetic prerequisites and signaling pathways promoting such partial epithelial-to-mesenchymal transitions (EMT) remain obscure. Here we report that murine intestinal organoids with hyperactive Wnt and MAPK signaling, and mutant Trp53 are purely epithelial and non-inv...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE159649 Epigenetic priming of enhancers underpins human germline competence and specification [ATAC-seq]
Contributor : Walfred W TangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGermline-soma segregation is a fundamental event during mammalian embryonic development. Here, we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced early priming of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. SOX17 is critical for both hPGCs and endoderm, in combination with l...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE159650 Epigenetic priming of enhancers underpins human germline competence and specification [ChIP-seq_Histone]
Contributor : Walfred W TangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGermline-soma segregation is a fundamental event during mammalian embryonic development. Here, we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced early priming of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. SOX17 is critical for both hPGCs and endoderm, in combination with l...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE159651 Epigenetic priming of enhancers underpins human germline competence and specification [ChIPseq_SOX17_PRDM1]
Contributor : Walfred W TangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGermline-soma segregation is a fundamental event during mammalian embryonic development. Here, we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced early priming of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. SOX17 is critical for both hPGCs and endoderm, in combination with l...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE159652 Epigenetic priming of enhancers underpins human germline competence and specification [RNAseq_SOX17_PRDM1_OE]
Contributor : Walfred W TangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGermline-soma segregation is a fundamental event during mammalian embryonic development. Here, we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced early priming of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. SOX17 is critical for both hPGCs and endoderm, in combination with lineage-specifi...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE159653 Epigenetic priming of enhancers underpins human germline competence and specification [RNAseq_WildType]
Contributor : Walfred W TangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGermline-soma segregation is a fundamental event during mammalian embryonic development. Here, we establish the epigenetic principles of human primordial germ cell (hPGC) development using in vivo hPGCs and stem cell models recapitulating gastrulation. We show that morphogen-induced early priming of mesendoderm enhancers transiently confers the competence for hPGC fate, but further activation favours mesoderm and endoderm fates. SOX17 is critical for both hPGCs and endoderm, in combination with lineage-specifi...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE159654 Sequential enhancer state remodelling defines human germline competence and specification
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE161052 The protective effect of spermine on diabetic cardiomyopathy.
Contributor : Can WeiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDiabetic cardiomyopathy (DCM) is a specific form of cardiomyopathy that is independent of coronary artery disease and hypertension. Exploring the transcriptomics and proteomics of DCM is of great significance for understanding the biology of the disease and for guiding new therapeutic targets for the potential therapeutic effect of spermine (SPM). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE165364 Heat shock-mediated global gene downregulation is achieved by premature transcription termination [TTchem-seq]
In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the regulation of U1snRNA and the disruption of U1-telescripting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE165365 Heat shock-mediated global gene downregulation is achieved by premature transcription termination [DRB_TTchem-seq]
In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the regulation of U1snRNA and the disruption of U1-telescripting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE165366 Heat shock-mediated global gene downregulation is achieved by premature transcription termination [FP_TTchem-seq]
In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the regulation of U1snRNA and the disruption of U1-telescripting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE165367 Heat shock-mediated global gene downregulation is achieved by premature transcription termination [4SU_mRNA-seq]
In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the regulation of U1snRNA and the disruption of U1-telescripting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE165368 Heat shock-mediated global gene downregulation is achieved by premature transcription termination
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE165584 Epigenome analysis of parent and radioresistant OSCC cells(OML1 and OML1R ).
Contributors : Michael Y Chan ; Hon-Yi Lin ; Shih-Kai Hung ; Ru-Inn LinSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome wide DNA methylation profiling changes in parent and radioresistant OSCC cells (OML1 and OML1R ) by The Illumina Infinium WG Methylation27. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE165856 Anorexia reduces energy expenditure in mice with lung cancer-induced cachexia
Contributors : Andre L Queiroz ; Marcus D GoncalvesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe defining feature of the cancer anorexia cachexia syndrome (CACS) is weight loss, which suggests a state of negative energy balance. It is unclear whether this net reduction in energy is due solely to anorexia or if a combination of anorexia and increased energy expenditure (EE) occurs. To address this issue, we measured the changes in body composition, food intake, and EE that occur following induction of lung cancer in mice. Mice with CACS developed severe atrophy in the white adipo...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE165984 Localization of wildtype Ioc4 in wildtype and set2 yeast strains. Localization of Ioc4 mutants (dPWWP, 2KE, dINS) in wildtype yeast strains.
Contributors : Michaela Smolle ; Madelaine GogolSeries Type : Genome variation profiling by genome tiling arrayOrganism : Saccharomyces cerevisiae ; Saccharomyces cerevisiae S288CChIP-chip assays to assess the localization of FLAG-tagged, wildtype and mutant Ioc4 in yeast. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Saccharomyces cerevisiae Saccharomyces cerevisiae S288C Source Type: research

GSE166111 Activation of the Mitochondrial ClpP protease is Synthetically Lethal with HDAC1/2 Inhibition in Glioblastoma Model Systems
Contributors : Thi T Nguyen ; Markus SiegelinSeries Type : Expression profiling by arrayOrganism : Homo sapiensBy integration of transcriptome and metabolite analyses, we showed that pharmacological activation of the mitochondrial ClpP protease through utilization of enhanced imipridone compounds (ONC206 and ONC212) in combination with global (Panobinostat) and selective (romidepsin) HDAC – inhibitors caused synergistic reduction of viability in established and patient-derived xenograft (PDX) cultures of human GBM. This effect occurred independent of TP53 status and was partially mediated by activation of a cell deat...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE166145 Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells (RNA-seq)
Contributors : Hegias Mira-Bontenbal ; Beatrice Tan ; Wilfred F van IJcken ; Joost GribnauSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRett Syndrome is a neurodevelopmental disorder in girls that is caused by heterozygous inactivation of the chromatin remodeler gene MECP2. Rett Syndrome may therefore be treated by reactivation of the wild type copy of MECP2 from the inactive X chromosome. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequa...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE166146 Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells (MeD-seq)
Contributors : Hegias Mira-Bontenbal ; Beatrice Tan ; Ruben Boers ; Joachim Boers ; Wilfred F van IJcken ; Joost GribnauSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusRett Syndrome is a neurodevelopmental disorder in girls that is caused by heterozygous inactivation of the chromatin remodeler gene MECP2. Rett Syndrome may therefore be treated by reactivation of the wild type copy of MECP2 from the inactive X chromosome. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluores...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE166147 Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells
Series Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE166185 SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE166495 ATAC-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.
Contributors : Anthony Leon ; Lucie Subirana ; Ildefonso Cases ; Manuel Irimia ; Juan J Tena ; Jose L Gomez-Skarmeta ; Hector Escriva ; Stephanie BertrandSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Branchiostoma lanceolatumThe goal of this projet was to identify genomic region showing differential accessibility between control and Activin-treated amphioxus explants at two time points (gastrula and neurula stage) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Branchiostoma lanceolatum Source Type: research

GSE166497 RNA-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.
Contributors : Anthony Leon ; Lucie Subirana ; Ildefonso Cases ; Manuel Irimia ; Juan J Tena ; Jose L Gomez-Skarmeta ; Hector Escriva ; Stephanie BertrandSeries Type : Expression profiling by high throughput sequencingOrganism : Branchiostoma lanceolatumThe goal of this projet was to identify genes differentially expressed between control and Activin-treated explants at two time points (gastrula and neurula stage) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Branchiostoma lanceolatum Source Type: research

GSE166498 Control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Branchiostoma lanceolatumThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Branchiostoma lanceolatum Source Type: research

GSE167466 Crosstalk between CRISPR-Cas9 and the human transcriptome
Contributors : Aaron A Smargon ; Assael A Madrigal ; Kevin D Dong ; Brian A Yee ; Gene W YeoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe find that CRISPR-Cas9 interacts reproducibly with hundreds of endogenous human RNA transcripts independent of its synthetic guide RNA (gRNA). This weak association (KD>100nM) can be explained partly by a computational model built on gRNA secondary structure and sequence. While Cas9-bound transcripts do not correlate with previously published genome-wide Cas9 cut-sites under gRNA co-expression in the model cell line, remarkably they correlate...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE171763 Inhibitors of Bcl-2 and Bruton ’s tyrosine kinase synergize to abrogate diffuse large B-cell lymphoma (DLBCL) growth
Contributors : Anne M üller ; Katrin BertramSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMethods: DLBCL cell lines RIVA, U-2932 and OCI-LY3 were treated in vitro with ibrutinib (Ibru) or dimethyl sulfoxide (DMSO). Additionally, RIVA and U-2932 were orthotopically transplanted into MISTRG mice and mice were treated for two weeks with Ibru or vehicle. Tumor cells were isolated from the bone marrow at the study endpoint. The total RNA was isolated and the mRNA profiles were generated by next-generation sequencing using the Illumina TruSeq mRNA stranded protocol.Results: We have c...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173798 Glucocorticoid inducton of DDIT4 transcription
Contributors : Jackson A Hoffman ; Kevin W Trotter ; Christopher R Day ; James M Ward ; Kaoru Inoue ; Joseph Rodriguez ; Trevor K ArcherSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThe hormone stimulated Glucocorticoid Receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. Here, we examined the effects of GR binding on enhancer dynamics and interrogated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhance...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE178464 The Transcriptional Response to Oxidative Stress is Independent of Stress-Granule Formation
Contributors : Amanjot Singh ; Arvind R Kandi ; Mani Ramaswami ; Baskar BakthavachaluSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterWe characterized oxidative-stress-induced transcriptional changes in Drosophila S2 cells and assessed how these were altered under conditions that disrupted stress granule (SG) assembly. Sodium-arsenite stress for 3 hours resulted predominantly in the induction or upregulation of stress-responsive mRNAs whose levels peaked during cell recovery after stress cessation. RNAi-mediated knock down of the conserved G3BP1/ Rasputin protein inhibited s...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE179705 Divergent molecular signatures of regeneration and fibrosis during wound repair
Contributors : Shamik Mascharak ; Heather E desJardins-Park ; Michael JanuszykSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRegeneration is the “holy grail” of tissue repair, but skin injury typically yields fibrotic, non-functional scars. Developing pro-regenerative therapies requires rigorous understanding of the molecular progression from injury to fibrosis or regeneration. Here, we report the divergent molecular events driving skin wound cells toward either scarring or regenerative fates. We profile scarring versus YAP inhibition-induced wound regeneration at the tra...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE181456 miRNA expression analysis of the hippocampus in a vervet monkey model of fetal alcohol spectrum disorder
Contributors : Rob F Gillis ; Roberta PalmourSeries Type : Non-coding RNA profiling by arrayOrganism : Chlorocebus aethiops ; synthetic constructAlcohol preferring vervet dams were permitted to ingest alcohol 4 days/week during the second half of gestation (e90-e165) and paired with sucrose matched controls. Cases and controls were sacrificed with subsequent hippocampal extraction at 5 months and 2 years. RNA was extracted according to the manufacturer's protocol and hybridized to the Affymetrix Rhesus Genechip microarray.We sought to identify whether global downregulation in mRNA dataset was related to miRNA expression in...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Chlorocebus aethiops synthetic construct Source Type: research

GSE184321 Cul5 regulates CD4+ T cell fate choice and allergic inflammation [RNA-seq]
Contributors : Binod Kumar ; Natania S Field ; Dale D Kim ; Asif A Dar ; Yanqun Chen ; Aishwarya Suresh ; Nadia Porter ; Christopher F Pastore ; Li Y Hung ; Keisuke Sawada ; Palak Shah ; Omar Elbulok ; Emily K Moser ; De'Broski R Herbert ; Paula M OliverSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAntigen encounter directs CD4+ T cells to differentiate into T-helper or -regulatory cells. This process focuses the immune response on the invading pathogen and limits tissue damage. Mechanisms that govern -helper versus -regulatory fate remain poorly understood. Here, we show that the E...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE186560 The 2 ´-O-methylation landscape of ribosomal RNA in Dictyostelium discoideum 
Contributors : Jan Diesend ; Ulf Birkedal ; Jonas Kjellin ; Jingwen Zhang ; Kim P Jablonski ; Fredrik S öderbom ; Henrik Nielsen ; Christian HammannSeries Type : OtherOrganism : Dictyostelium discoideumA sequencing-based profiling method (RiboMeth-seq) for ribose methylations was applied to study methylation patterns in Dictyostelium discoideum (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Other Dictyostelium discoideum Source Type: research

GSE188216 barley responses to nitrate limitation-BarIEy Stress Tolerance
Contributors : Jos é Caius ; Alia- Dellagi ; Ludivine Taconnat-SoubigouSeries Type : Expression profiling by high throughput sequencingOrganism : Hordeum vulgarengs2020_19_arimnet-barley responses to nitrate limitation-What are the molecular mechanisms taking place in barley under nitrate limitation?-Barley were grown on sand under 0.5 mM nitrate (Low nitrate= LN) or 5 mM nitrate (high nitrate = HN) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Hordeum vulgare Source Type: research

GSE188541 Patient-Derived Liver on Chips
Contributors : Jonathan Z Sexton ; Charles J Zhang ; Matthew J O'Meara ; Sophia R MeyerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensiPSCs were differentiated to human liver organoids as previously described. Human liver organoids were dispersed into single-cell suspension with trypsin (0.25%) and transferred to both channels in an dual-channel organ on chip system and cultured in hepatocyte maturation media. Media flow was regulated to 30 µL/hr for both channels. After 7 days of culture, liver chips were treated with vehicle control, or DILI-related compounds APAP, FIAU, teno...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE189562 Heat Shock induces premature transcript termination and reconfigures the human transcriptome
In this study, we demonstrate that transcription downregulation during Heat shock is mainly achieved by premature transcription termination through the disruption of telescripting. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE189729 EP400NL plays role in polyamine synthesis and mitochondrial biogenesis for the cell growth
Contributors : Jeong H Park ; Jaehoon Kim ; Hyoungmin KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo identify EP400NL-responsive genes by RNA expression profiling, tetracycline-induced Flp-In T-Rex cell line was used without additional serum and IFN γ-stimulation to avoid a universal upregulation of genes. In this condition, most of the genes were differentially expressed less than 1.5-fold range. The 121 genes with over 1.5-fold differential upregulations were further analysed by gene ontology. The result indicates that EP400NL upregulation s eems to enhance housekeeping...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE189905 Neuradapt: Structural Optimization and Transcriptomic Analysis
Contributors : Andrey Poloznikov ; Sergey Nikulin ; Dmitry Hushpulian ; Anna Khristichenko ; Andrey Ossipyants ; Vladimir Tishkov ; Irina GazaryanSeries Type : Expression profiling by arrayOrganism : Homo sapiensA newly developed “branched tail” oxyquinoline, neuradapt, and its variants are an order of magnitude more effective HIF prolyl hydroxylase (HIF PHD) inhibitors than roxadustat and vadadustat in HIF1 ODD-luc reporter assay. Structure-activity relationships and computer modeling for the oxyquinoline inhibitors poi nt to the plausible engagement of the pyridine ring nitrogen in interaction with Asp254 res...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE190134 Human iPSC-Derived Fallopian Tube Organoids with BRCA1 Mutation Recapitulate Early Stage Carcinogenesis
Contributors : Michael J Workman ; Nur Yucer ; Clive N SvendsenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe generate induced pluripotent stem cells (iPSCs) from healthy individuals and young ovarian cancer patients with germline pathogenic BRCA1 mutations. We then differentiate them into a human iPSC-derived fallopian tube organoid model. We recapitulated BRCA1 mutant ovarian carcinogenesis in vitro and showed tumors in vivo. Using the IPSC derived fallopian tube organoid model, we identify a unique transcriptional profile associated with BRCA1 mutation similar to the ovarian ca...
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE192683 Amino acids and IGF1 regulation of fish muscle growth revealed by transcriptome and microRNAome integrative analyses of pacu (Piaractus mesopotamicus) myotubes
Series Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Piaractus mesopotamicusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Piaractus mesopotamicus Source Type: research

GSE193625 Astrocyte immunosenescence in IL-10 and cholesterol signaling in the aged brain impairs microglial regulation following peripheral immune activation
Contributors : Shane M O'Neil ; Emma E Hans ; Starr Jiang ; Lynde M Wangler ; Jonathan P GodboutSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe purpose of this study was to determine the cell-, age-, and time-specific transcriptional profiles of cells within the brain after peripheral immune challenge with lipopolysaccharide. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE193829 Next Generation Sequencing of Saline and Methamphetamine-treated Mouse Hippocampus Transcriptomes
Contributors : Fengrong Chen ; Juehua YuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived hippocampus transcriptome profiling (RNA-seq) in mouse to evaluate alterations in hippocampus with methamphetamine administrations. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE193984 Next Generation Sequencing Facilitates Quantitative Analysis of N. crassa Wild Type, stk-17ko and stk-17com Transcriptomes treated with or without ketoconazole
Contributors : Chengcheng Hu ; Mi Zhou ; Xianhe Cao ; Wei Xue ; Zhenying Zhang ; Shaojie Li ; Xianyun SunSeries Type : Expression profiling by high throughput sequencingOrganism : Neurospora crassaSTK-17, a kinase that responses to azoles transcriptionally, is required for azole resistance. By analyzing and comparing the transcriptomes from samples of N. crassa Wild Type, stk-17ko and stk-17com strain treated with or without ketoconazole, the biological processes that would be affected by stk-17 deletion was revealled. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 24, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Neurospora crassa Source Type: research