GSE115319 Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Third-party reanalysisOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Third-party reanalysis Homo sapiens Source Type: research

GSE115773 Real-time quantitative PCR analysis of serum from osteoporotic Mexican women
Contributors : Eric G Ram írez-Salazar ; Sergio Carrillo-Patiño ; Alberto Hidalgo-Bravo ; Berenice Rivera-Paredez ; Manuel Quiterio ; Paula Ramírez-Palacios ; Nelly Patiño ; Margarita Valdés-Flores ; Jorge Salmerón ; Rafael Velázquez-CruzSeries Type : Expression profiling by RT-PCROrganism : Homo sapiensRNA was purified from serum of osteoporotic and healthy postmenopausal mexican women using miRNeasy Serum/Plasma kit (QIAGEN). For microRNA expression analysis we used the Human MicroRNA A+B Cards Set v3.0 TaqMan Low Density Array platform (Applied Biosystems). Analysis was p...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by RT-PCR Homo sapiens Source Type: research

GSE116330 Small RNA libraries
Contributors : Javier F Palatnik ; Blake Meyers ; Bel én Moro ; Uciel ChorosteckiSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Arabidopsis thalianaMany evolutionarily conserved miRNAs in plants regulate transcription factors with key functions in plant development. Hence, mutations in core components of the miRNA biogenesis machinery causes strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from an arm of the fold-back precursor. Defects in the selection of the correct miRNA sequence will ultimately affect miRNA target specificity,...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE116376 Specific Parallel Analysis of RNA End and Small RNA libraries
Series Type : Non-coding RNA profiling by high throughput sequencingOrganism : Arabidopsis thalianaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE119122 Transcriptomic profiles of tissues from rats treated with drug combinations [Study 1]
Contributors : Myrtle Davis ; Pierre R BushelSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusCombinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound ’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objec...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE119129 Transcriptomic profiles of tissues from rats treated with drug combinations [Study 2]
Contributors : Myrtle Davis ; Pierre R BushelSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusCombinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound ’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objec...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE119133 Transcriptomic profiles of tissues from rats treated with drug combinations [Study 3]
Contributors : Myrtle Davis ; Pierre R BushelSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusCombinations of anticancer agents may have synergistic anti-tumor effects, but enhanced toxicity often limit their clinical use. The risk that combinations of two or more drugs will cause adverse effects that are more severe than drugs used as monotherpies can be hypothesized from comprehensive analysis of each compound ’s activity. We generated microarray gene expression data following a single dose of agents administered individually with that of the agents administered in a combination. The key objec...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE119135 Transcriptomic profiles of tissues from rats treated with drug combinations
Series Type : Expression profiling by arrayOrganism : Rattus norvegicusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE119702 Effect of Fbxo22 on ER and SRC-3 recruitment to the genomic loci
Contributors : Yoshikazu Johmura ; Makoto NakanishiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe agonistic/antagonistic bio-character of selective estrogen receptor modulators (SERMs) can have therapeutic advantages, particularly in the case of premenopausal breast cancers. Although the contradictory effects of these modulators have been studied in terms of cross-talk between estrogen receptor (ER)-coactivator dynamics and growth factor signaling, the molecular basis of these mechanisms is still obscure. We demonstrate here an unidentified series of regulatory mech...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE119705 Adenosinergic signaling alters natural killer cell functional responses
Contributors : Andrea M Chambers ; Nadia A Lanman ; Jiao Wang ; Hao Yu ; Sandro Matosevic ; Kyle B LupoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: The goal of this study was to globally characterize the transcript levels of genes NK cells in the presence or absence of adenosine (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE119714 Regulatory mechanisms of brown rot genes for responding to environmental carbon signals in Postia placenta
Contributors : Jiwei Zhang ; Hugh D Mitchell ; Lye M Markillie ; Galya Orr ; Jonathan S Schilling ; Matthew GaffreySeries Type : Expression profiling by high throughput sequencingOrganism : Postia placentaBrown rot fungi evolved the unique strategy to efficiently decay wood structures and selectively extract carbohydrates, and this involved the sophistical regulation of functional genes (Zhang et al., PNAS, 2016, 113: 10968-). However, the regulatory mechanisms of brown rot genes were not well known, impeding the implication and application of brown rot machinery in biomass conversions. In this work, we systematically stud...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Postia placenta Source Type: research

GSE119725 Differential effects of a glucagon-like peptide 1 receptor agonist in NAFLD and in response to hepatectomy
Contributors : M P Valdecantos ; Laura Ruiz ; Angela M.ValverdeSeries Type : Expression profiling by arrayOrganism : Mus musculusThe genomic analysis of liver from mice fed with standard or MCD diet and treated with FC-GLP-1 during two weeks before 70%partial hepatectomy (PH) and after 2 weeks PH resulted in a set of genes regulated by diet and other set regulated differentially by treatment in MCD treated animals. These genes are apparently responsible for the reversion and prevention of NAS and improvement in hepatic regeneration induced by drug treatment (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE119738 Barcoded DNA sequencing (BarSeq) samples from passaging of Caulobacter crescentus in medium containing cheesecloth
Contributors : David M Hershey ; Sean CrossonSeries Type : OtherOrganism : Caulobacter vibrioidesBarSeq experiment enriching for C. crescentus mutants that do not adhere to cheesecloth. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Other Caulobacter vibrioides Source Type: research

GSE119747 Comparison of enteroendocrine cells and pancreatic β-cells using gene expression profiling and insulin gene methylation
In this study, similarities between EECs and β-cells were evaluated in detail. To obtain specific subtypes of EECs, cell sorting by flow cytometry was conducted from STC-1 cells (a heterogenous EEC line), and each single cell was cultured and passaged. Five EEC subtypes were established according to hormone expression, measured by quantitativ e RT-PCR and immunostaining: L, K, I, G and S cells expressing glucagon-like peptide-1, glucose-dependent insulinotropic polypeptide, cholecystokinin, gastrin and secretin, respectively.Global microarray gene expression profiles revealed a higher similarity between each EEC subty...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE119754 Transcriptomic Signature of Right Ventricular Failure in Experimental Pulmonary Arterial Hypertension: Deep Sequencing Demonstrates Mitochondrial, Fibrotic, Inflammatory and Angiogenic Abnormalities
Contributors : Francois Potus ; Charles C Hindmarch ; Kimberly J Dunham-Snary ; Jeff Stafford ; Stephen L ArcherSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusAbstract: Right ventricular failure (RVF) remains the leading cause of death in pulmonary arterial hypertension (PAH). We investigated the transcriptomic signature of RVF in hemodynamically well-phenotyped monocrotaline (MCT)-treated, male, Sprague-Dawley rats with severe PAH and decompensated RVF (increased right ventricular (RV) end diastolic volume (EDV), decreased cardiac output (CO), tricuspid annular plane systolic e...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE119763 Exploring the spatiotemporal genetic heterogeneity in metastatic lung adenocarcinoma using a nuclei flow-sorting approach
Contributors : Thomas Lorber ; Noemi Andor ; Tanja Dietsche ; Valeria Perrina ; Darius Juskevicius ; Karen Pereira ; Stephanie U Greer ; Arthur Krause ; David Mueller ; Spasenija S Prince ; Didier Lardinois ; Michael T Barrett ; Christian Ruiz ; Lukas BubendorfSeries Type : Genome variation profiling by genome tiling arrayOrganism : Homo sapiensVariable tumor cellularity can limit sensitivity and precision in comparative genomics, because differences in tumor content can result in misclassifying truncal mutations as region-specific private mutations in stroma-rich regions, especially when studying tissue specimens of medio...
Source: GEO: Gene Expression Omnibus - September 11, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Homo sapiens Source Type: research

GSE119662 Genetic modifier of TGF-beta1 stimulated pulmonayr fibrosis
Contributors : Jack A Elias ; Chun G Lee ; Chang-Min LeeSeries Type : Expression profiling by arrayOrganism : Mus musculusExpression profiling of pulmonayr fibrosis prone and fibrosis resistant strains of mice with transgenic overexpression of TGF-beta1 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE72912 ZnO-nanoparticles induce changes in the expression of genes associated with stress responses in spinach (Spinacia oleracea) without affecting Zn uptake
Conclusions: A de novo transcriptome was developed for spinach. When spinach plants were exposed to ZnO nanoparticles, they seem to sense the nanoparticles similarly to external chemicals or pathogens and induced production of reactive oxygen species. Hormone signaling pathways were activated leading to the induced expression of hormones with different roles in defense. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Spinacia oleracea Source Type: research

GSE75086 Cellular and Molecular Targeting of Recurrence in Acute Myeloid Leukemia
Contributors : Allison Boyd ; Lili Aslostovar ; Aline Fiebig-Comyn ; Zoya Shapovalova ; Mohammed Almakadi ; Jenniffer Reid ; Fanny Casado ; Kyle Salci ; Anargyros Xenocostas ; Ronan Foley ; Brian Leber ; Mickie BhatiaSeries Type : Expression profiling by arrayOrganism : Homo sapiensWhile disease recurrence remains the outstanding clinical challenge in acute myeloid leukemia (AML), the basis of relapse remains poorly characterized and thereby preventing effective therapeutic targeting. We performed gene expression analysis of human AML patient samples in addition to in vitro and in vivo assays of leukemic cell survival and ...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104079 Metabolic and Molecular Framework for the Enhancement of Endurance by Intermittent Fasting
Contributors : Krisztina Marosi ; Keelin Moehl ; Ignacio Navas-Enamorado ; Sarah J Mitchell ; Yongqing Zhang ; Elin Lehrmann ; Miguel A Aon ; Sonia Cortassa ; Kevin G Becker ; Mark P MattsonSeries Type : Expression profiling by arrayOrganism : Mus musculusEvolutionary considerations suggest that the body has been optimized to perform at a high level in the fasted state when fatty acids and their ketone metabolites are a major fuel source for muscle cells. Because fasting is the most potent physiological stimulus for ketosis, we designed a study to determine the impact of intermittent fasting during endurance training on pe...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE108995 Profiling of escape kinetics of viruses subjected to RNAi
Contributor : Benjamin R tenOeverSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Canis lupus familiaris ; Homo sapiens ; Mesocricetus auratusTo assess how viruses of different genome compositions escape engineered RNAi (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Canis lupus familiaris Homo sapiens Mesocricetus auratus Source Type: research

GSE110669 Transcriptional profiles of normal human mature B cells
Contributors : Katia Basso ; Antony Baden Holmes ; Riccardo Dalla-FaveraSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMature B cells leave the bone marrow as na ïve B cells and migrate to the secondary lymphoid organs where they encounter the antigen for the first time. This interaction stimulates B cells to rapidly grow and form characteristic histological structures called germinal center. In the germinal centers, B cells are targeted by mechanisms of ge netic editing of the immunoglobulin loci, namely somatic hypermutation and class switch recombination, undergo selection fo...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110676 Germinal Center B cell transcriptional profiles in Mef2b mouse models
Contributors : Katia Basso ; Antony Baden Holmes ; Riccardo Dalla-FaveraSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe MEF2B transcription factor is recurrently mutated in germinal-center (GC)-derived B-cell lymphomas, but its role in normal and neoplastic GC development is unknown. Here we identify MEF2B transcriptional targets in GC, which indicate its control of cell proliferation, apoptosis, GC confinement and differentiation. Consistently, Mef2b deletion reduces GC formation in mice. The most common tumor-associated MEF2B mutant (MEF2BD83V) is hypomorphic, but escapes bindin...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE110682 MEF2B chromatin binding in normal and malignant B cells
Contributors : Katia Basso ; Antony B Holmes ; Riccardo Dalla-FaveraSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe MEF2B transcription factor is recurrently mutated in germinal-center (GC)-derived B-cell lymphomas, but its role in normal and neoplastic GC development is unknown. Here we identify MEF2B transcriptional targets in GC, which indicate its control of cell proliferation, apoptosis, GC confinement and differentiation. Consistently, Mef2b deletion reduces GC formation in mice. The most common tumor-associated MEF2B mutant (MEF2BD83V) is hypomorphic, but esca...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111652 Transcriptome analysis of U87 cells upon LINC00152 knockdown
Contributors : Brian J Reon ; Bruno T Karia ; Manjari Kiran ; Anindya DuttaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo understand the global changes in genes expression after knockdown of LINC00152, we compared transcriptomes of control cells (treated with siGL2) and LINC00152 knockdown cells (treated with si00152). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111940 Hydroxyurea protects hippocampal neurons against oxidative, metabolic and excitotoxic stress, and improves spatial memory in a mouse model of Alzheimer ’s disease (Mouse)
Contributors : Rebecca D Brose ; Elin Lehrmann ; Yongqing Zhang ; Kirby D Smith ; Mark P MattsonSeries Type : Expression profiling by arrayOrganism : Mus musculusAlzheimer ’s disease (AD) is an age-related neurodegenerative disorder characterized by accumulation of amyloid β-peptide (Aβ) plaques in the brain and decreased cognitive function leading to dementia. We determined if hydroxyurea (HU), a ribonucleotide reductase inhibitor known to activate adaptive cellu lar stress responses in fibroblasts, could protect rat hippocampal neurons against oxidative-, excitatory-, mitochondrial-, and Aβ-induced s...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE111941 Hydroxyurea protects hippocampal neurons against oxidative, metabolic and excitotoxic stress, and improves spatial memory in a mouse model of Alzheimer ’s disease (Rat)
Contributors : Rebecca D Brose ; Elin Lehrmann ; Yongqing Zhang ; Kirby D Smith ; Mark P MattsonSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusAlzheimer ’s disease (AD) is an age-related neurodegenerative disorder characterized by accumulation of amyloid β-peptide (Aβ) plaques in the brain and decreased cognitive function leading to dementia. We determined if hydroxyurea (HU), a ribonucleotide reductase inhibitor known to activate adaptive cellu lar stress responses in fibroblasts, could protect rat hippocampal neurons against oxidative-, excitatory-, mitochondrial-, and Aβ-indu...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE111943 Hydroxyurea attenuates oxidative, metabolic, and excitotoxic stress in rat hippocampal neurons and improves spatial memory in a mouse model of Alzheimer ’s disease
Series Type : Expression profiling by arrayOrganism : Mus musculus ; Rattus norvegicusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Rattus norvegicus Source Type: research

GSE115571 Single-cell transcriptomics reveals distinct microglia signatures under inflammation
Contributors : Carole Sousa ; Suresh K Poovathingal ; Tony Kaoma ; Francisco Azuaje ; Alexander Skupin ; Alessandro MichelucciSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMicroglia are specialized parenchymal-resident phagocytes of the central nervous system (CNS) that actively support, defend and modulate the neural environment. Dysfunctional microglia responses are believed to worsen CNS diseases, nevertheless their impact during the neuroinflammatory processes remains largely obscure. Here, using a combination of multicolor flow cytometry and single-cell RNA sequencing, we compr...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116224 Small RNA-seq analysis shows reduced tRNA levels in cdk1-as1 mutants
Contributors : Jorrit Enserink ; Carmen M HerreraSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaePurpose: Determine whether Cdk1 only regulates a specific subset of tDNAs, or whether Cdk1 has a more global impact on tDNA expression; Method: We study the expression of tRNA genes in WT cells and cdk1-as1 mutants during S phase by small-RNAseq; Result: We found that expression of at least 77% of all tDNAs is significantly downregulated in S-phase in the cdk1-as1 mutant compared with the WT strain; Conclussions: Cdk1 promotes transcription of the majority of tRNA genes dur...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE118305 Genome-wide RNA-seq and Epigenetic analysis of human monocyte derived macrophage responses to Zika virus infection
Contributors : Aaron F Carlin ; Sujan Shresta ; Christopher K GlassSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensInterpretation of genome-wide investigations of host-pathogen interactions are often obscured by analyses of mixed populations of infected and uninfected cells. Thus, we developed a system whereby we simultaneously characterize and compare genome-wide transcriptional and epigenetic changes in pure populations of virally-infected and neighboring uninfected cells to identify viral-regulated host-responses. U...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE119530 RNA expression in postnatal mouse ventricular tissue
This study aims at providing an integrated resource of mRNA, protein and metabolite changes in the neonatal heart to identify metabolism-related mechanisms associated with the postnatal loss of regenerative capacity. Mouse ventricular tissue samples taken on postnatal days 1, 4, 9 and 23 (P01, P04, P09 and P23, respectively) were analyzed with RNA sequencing (RNAseq) and global proteomics and metabolomics. Differential expression was observed for 8547 mRNAs and for 1199 of the 2285 quantified proteins. Furthermore, 151 metabolites with significant changes were identified. Gene ontology analysis, KEGG pathway analysis and f...
Source: GEO: Gene Expression Omnibus - September 10, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE119689 Spo11-oligo mapping in wild type S. cerevisiae strain
Contributors : Megan van Overbeek ; Scott KeeneySeries Type : OtherOrganism : Saccharomyces cerevisiaeTo segregate accurately during meiosis, homologous chromosomes in most species must recombine. Very small chromosomes would risk missegregation if recombination were randomly distributed, so the double-strand breaks (DSBs) that initiate recombination are not haphazard. How this nonrandomness is controlled is not understood. Here we demonstrate that Saccharomyces cerevisiae integrates multiple, temporally distinct pathways to regulate chromosomal binding of pro-DSB factors Rec114 and Mer2, thereby controlling duration of a ...
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE72862 Next Generation Sequencing Facilitates Quantitative Analysis of mesoderm posterior bHLH transcription factor 1(MESP1)+ and MESP1- cells' Transcriptomes
Conclusions: the gene expression profile of MESP1-mTomato cells indicates that they are cardiovascular progenitor cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104728 Proteogenomic landscape of medulloblastoma subgroups [methylation]
In this study we present the first analysis regrouping genomic and methylation status, whole-transcriptome sequencing and quantitative proteomics. First, our proteomic analysis clarified medulloblastoma subgroup identity. Second, analysis of proteome and phosphoproteome highlighted disregulated signalling pathways that have not been predicted by transcriptomic analysis. Altogether, combined multi-scale analyses of medulloblastoma have allowed us to identify and prioritize novel molecular drivers involved in human medulloblastoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE107508 Proteogenomic landscape of medulloblastoma subgroups [SNP]
In this study we present the first analysis regrouping genomic and methylation status, whole-transcriptome sequencing and quantitative proteomics. First, our proteomic analysis clarified medulloblastoma subgroup identity. Second, analysis of proteome and phosphoproteome highlighted disregulated signalling pathways that have not been predicted by transcriptomic analysis. Altogether, combined multi-scale analyses of medulloblastoma have allowed us to identify and prioritize novel molecular drivers involved in human medulloblastoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array SNP genotyping by SNP array Homo sapiens Source Type: research

GSE107511 Proteogenomic landscape of medulloblastoma subgroups
Series Type : Methylation profiling by genome tiling array ; Genome variation profiling by SNP array ; SNP genotyping by SNP arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Genome variation profiling by SNP array SNP genotyping by SNP array Homo sapiens Source Type: research

GSE117055 Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system
Contributors : Charles Petitpr é ; Haohao Wu ; Anil Sharma ; Anna Tokarska ; Paula Fontanet ; Yiqiao Wang ; Françoise Helmbacher ; Kevin Yackle ; Gilad Silberberg ; Saida Hadjab ; François LallemendSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSpiral ganglion (SG) neurons of the cochlea convey all auditory inputs to the brain, yet the cellular and molecular complexity necessary to decode the various acoustic features in the SG has remained unresolved. Using unbiased single-cell RNA sequencing, we identified four types of SG neurons, including three novel subclas...
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE119684 A Trio Based Approach to Epilepsy Methylome
Contributor : Ozkan OzdemirSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome-wide methylation profiling on 15 Father-Mother-Offspring trios with Genetic Generalized Epilepsies. All trios have 2 affected (1 parent and offspring) and 1 healthy individuals. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles which has probes for aproximetely 450000 CpG loci. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE119687 Beta-catenin dependent gene expression
Contributor : Susan D ReynoldsSeries Type : Expression profiling by arrayOrganism : Mus musculusGene experssion was evaluated in the lungs of mice in which beta-catenin was stabilized or knocked out in the SCGB1A1 lineage.Gene expression was assayed on post-natal day 21 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE119650 Transcriptomes of microglia in experimental cerebral malaria in mice in the presence and absence of Type I Interferon signaling
Contributors : Jean Langhorne ; Carlos T Lopez ; Richard Mitter ; Jingwen Lin ; Barbara CapucciniSeries Type : Expression profiling by arrayOrganism : Mus musculusPlasmodium berghei ANKA infection in mice is used as a model for human cerebral malaria, the most severe complication of Plasmodium falciparum infection. The response of brain cells such as microglia has been little investigated, and may play a role in the pathogenesis or regulation of cerebral malaria. We showed previously that microglia are activated in P. berghei infections, and that Type 1 Interferon signaling is important for activation. This dataset contai...
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE73055 Expression data from hela cells stable clones overexpressing TFEB-GFP
Contributor : Rossella De CegliSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn order to identify the effects of TFEB overexpression on the hela cells transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the hela TFEB stable clonesTranscriptome analysis of hela stable clones overexpressing TFEB-GFP (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE95806 Expression data from acd, p53 and double mutant mouse embryos
Contributors : Ceren Sucularli ; Catherine E KeeganSeries Type : Expression profiling by arrayOrganism : Mus musculusIn mouse, the adrenocortical dysplasia (acd) phenotype shows limb and body axis anomalies, as a result of p53-dependent apoptosis, and perinatal lethality. The p53 deficiency partially rescues anomalies, but not perinatal lethality, implicating the involvement of p53-independent mechanisms in the acd phenotype. Differentially expressed genes in acd mutant and double mutant embryos were identified. p53-dependent and –independent pathways contributing to acd phenotype were characterized.We used microarra...
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE101567 Global gene-expression profiles of WT Arabidopsis (Col-0), npr1-1, and hac1/5 treated with water or INA
Contributors : Yoo-Sun Noh ; Bosl Noh ; Hongshi Jin ; Sun-Mee Choi ; Min-Jeong Kang ; Se-Hun Yun ; Dong-Jin KwonSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaGlobal gene-expression profiles of WT Arabidopsis (Col-0), npr1-1, and hac1/5 were generated by RNA seq to study functional relationship between NPR1 and HACs in plant defense (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE101570 Genome-wide maps of histone H3 acetylation (H3Ac) in wild type (WT; Col-0), npr1-1, and hac1/5
Contributors : Yoo-Sun Noh ; Bosl Noh ; Hongshi Jin ; Sun-Mee Choi ; Min-Jeong Kang ; Se-Hun Yun ; Dong-Jin KwonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaGenome-wide H3Ac maps of WT (Col-0), npr1-1, and hac1/5 leaves were generated by chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP seq) to understand the role of HATs in the reprogramming of the epigenome during immune response. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE101572 HTS-Seq analysis of wild type (WT; Col-0), npr1-1, and hac1/5
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE103578 lncRNA and mRNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients
Contributors : Xu Hanshi ; Xiao Youjun ; Zou YaoyaoSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensFibroblast-like synoviocytes (FLSs) are critical for synovial aggressiveness and joint destruction in rheumatoid arthritis (RA).The role and expression patterns of long noncoding RNAs (lncRNAs) in RA are largely unknown. We performed lncRNA and mRNA microarrays to identify differentially expressed lncRNAs and mRNAs in fibroblast-like synoviocytes from rheumatoid arthritis patients compared with fibroblast-like synoviocytes from trauma patients. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE103621 Microarray analysis of Human Epidermal Keratinocytes, neonatal (HEKn) exposed to solar-simulated visible and ultraviolet radiation with and without sunscreen protection.
Contributor : Sami QutobSeries Type : Expression profiling by arrayOrganism : Homo sapiensKertinocyte cultures grown in 60 mm petri dishes were placed 186 mm from the solar simulator source (Solar-simulated ultraviolet radiation 1600W Xenon short arc lamp with an Oriel Air Mass 1 Direct Filter, (AM1:D:B; model 81074) and KG2 Short Pass Filter. irradiance 9.84 mW/cm ² for UVA (98.3%), 0.174 mW/cm² for UVB (1.7%) and 10 mW/cm² (0.017 mW/cm² erythemally-weighted) for the total UVR irradiance) and received a dose of either 0, 10, 20 and 150 kJ/m2 of unweighted ultraviolet radiation and 0, 10 and 150 kJ/m2 o...
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE105206 Variant PRC1 competes with retinoic acid-related signals to repress Meis2 in distal forelimb bud
Contributors : N Yakushiji-Kaminatsui ; H KosekiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusSuppression of Meis genes in the distal limb bud is required for Proximal-Distal (PD) specification of the forelimb. Polycomb group (PcG) factors play a role in downregulation of retinoic acid (RA)-related signals in the distal forelimb bud, causing Meis repression. It is, however, not known if downregulation of RA-related signals and PcG-mediated proximal genes repression are functionally linked. Here, we reveal that PcG factors and RA-related signals antagonize each other to...
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE110256 Transcriptomic RNAseq drug screen in cerebrocortical cultures; towards novel neurogenetic disease therapies.
Contributors : Jeremiah A Hadwen ; Sarah Schock ; Alan J Mears ; Robert Yang ; Philippe Charron ; Liying Zhang ; Hualin S Xi ; Alex E MacKenzieSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRare monogenic diseases affect millions worldwide; although over 4,500 rare disease genotypes are known, disease-modifying drugs are available for only 5% of them. The sheer number of these conditions combined with their rarity precludes traditional costly drug discovery programs. An economically viable alternative is to repurpose established drugs for rare diseases. Many genetic diseases result f...
Source: GEO: Gene Expression Omnibus - September 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research