GSE117268 Mapping of regions that are systematically under-replicated during cell cycle stages
Series Type : Genome variation profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE30730 Argonaute-miRNA complexes reveal concerted action in disease related pathways of a human, glioblastoma cell line
In this study, the regulation of glioblastoma-relevant pathways by small non-coding RNAs was analyzed by identification of Argonaute protein-associated microRNAs and mRNAs. We utilized a highly controlled method termed PAR-CLIP-Array by biochemical isolation of cross-linked ribonucleoprotein complexes with monoclonal antibodies specific for individual Argonaute proteins followed by microarray detection. We demonstrate here that the different Argonaute proteins bind different subsets of miRNAs and mRNAs in a glioblastoma cell line model. By extending our study generating miRNA-mRNA network interaction models we could furthe...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Mus musculus Rattus norvegicus synthetic construct Source Type: research

GSE93833 Basal hair follicle stem cell mRNA expression levels of mice at 3, 19 and 24 months of age
Contributors : Bill Keyes ; Mari-Carmen OrtellsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAnalysis of gene signatures on HFSCs (CD49f High/Cd34+) during normal chronological aging. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE99258 Transcriptome analysis of C2C12 cells (WT and MYOD KO) overexpressing MUNC: proliferating and differentiating conditions.
Contributors : Magdalena A Cichewicz ; Manjari Kiran ; Roza K Przanowska ; Anindya DuttaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo check global changes of genes expression correlating with induction of MUNC, we stably overexpressed MUNC in WT cells and in MYOD KO cells. We compared transcriptomes of control cells and cells overexpressing MUNC and distinguished genes that are differentially expressed in different conditions (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE101550 Essential roles of mitochondria biogenesis regulator Nrf1 in retina development and homeostasis
Contributors : Chai-An Mao ; Takae KiyamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: RNA-seq analysis for E13.5 wildtype vs. Nrf1-flox/flox:Six3-Cre retinas (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE101599 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and transgenic DgWRKY5 Chrysanthemum Transcriptomes
Contributor : L YuSeries Type : Expression profiling by high throughput sequencingOrganism : Chrysanthemum x morifoliumWe generated 12 Gb of high-quality sequencing data (~6 Gb per sample) to clarify the molecular mechanism of salt tolerance between wild tipe and transgenic DgWRKY5 chrysanthemum under normal condition. A total of 1078 differentially expressed genes (DEGs) (593 up-regulated and 485 down-regulated) were identified between CK and DgWRKY5, including genes encoding transcription factors and protein kinases. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and st...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Chrysanthemum x morifolium Source Type: research

GSE107250 Study of ribosome dynamics after osmotic stress in Lsm1 and Pat1 deletions
In this study, we aim to understand how the fates of stress-activated mRNAs are determined under stress conditions by isolating individual osmostress-activated mRNA species, quantitating the proteins associated in vivo with each of them, and analyzing how deletion of these proteins impact on the expression of stress-activated genes. By comparison with the proteome associated with individual not stress-related mRNA species, we show specific proteins to be preferentially binding to osmostress-activated mRNAs, notably members of the cytoplasmic Pat1 / Lsm1 – 7 complex. We evaluated the impact of this complex on the stre...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE108986 PKR senses nuclear and mitochondrial signals by interacting with endogenous double-stranded RNAs
Contributors : Yoosik Kim ; Joha Park ; V N KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensProtein kinase RNA-activated (PKR) induces immune response by sensing viral double-stranded RNAs (dsRNAs). However, growing evidence suggests that PKR can also be activated by endogenously expressed dsRNAs. Here, we capture these dsRNAs by formaldehyde-mediated crosslinking and immunoprecipitation-sequencing and find that various noncoding RNAs interact with PKR. Surprisingly, the majority of the PKR-interacting RNA repertoire is occupied by mitochondrial RNAs (mtRNAs). MtRNAs can form inter...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109370 Deregulation associated with cardiac conduction defects in Myotonic Dystrophy Type 1 using TU-Tagging
Contributors : Emilie Plantie ; Lucie PicchioSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterTotal RNA was extracted from about 10, 1-week or 5-weeks old, entire or dissected (head, legs, wings and ovaries removed) adult flies, using TRIzol reagent (Invitrogen) following manufacturer ’s instructions. The following genotypes dedicated for TU-tagging cell - specific transcript isolation were used: Hand>LacZ;HA-UPRT, Hand>MblRNAi;HA-UPRT, Hand>Bru3;HA-UPRT and Hand>960CTG;HA-UPRT (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE115860 Transcriptional profiling of mouse plasma cells
Series Type : Expression 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 - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116237 Towards minimal residual disease-directed therapy in melanoma
Contributors : Sara Aibar ; Daniel Brown ; Florian RambowSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensMany patients with advanced cancers achieve dramatic responses to a panoply of therapeutics, yet retain minimal residual disease (MRD), which ultimately results in relapse. To gain insights into the biology of MRD we applied single-cell RNA-sequencing to malignant cells isolated from BRAF-mutant patient-derived xenograft (PDX) melanoma cohorts exposed to concurrent RAF/MEK-inhibition. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE117137 Inhibition of Neogenin Fosters Resolution of Inflammation and Tissue Regeneration
Contributors : Valbona Mirakaj ; Andreas K örnerSeries Type : Protein profiling by protein arrayOrganism : Mus musculusProtein and phosphorylation (TGF- β Phospho Antibody Array, FullMoonBioscience, #PTG176) profiling of peritoneal monocytes (pooled lavages from 4 mice / condition) was carried out according to the manufacturer’s instructions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Protein profiling by protein array Mus musculus Source Type: research

GSE117160 Inhibition of the Aryl Hydrocarbon Receptor - Polyamine Biosynthesis Axis Suppresses Multiple Myeloma and prostate cancer progression
This study identified a previously unrecognized regulatory axis between AHR and polyamine metabolism and discovered clofazimine as an inhibitor of AHR and a potentially clinically-relevant anti-multiple myeloma agent.RNA-seq: human multiple myeloma MM1S and human normal fibroblasts WI38 cells -/+ CLF 2-4uM for 24hrs; -/+ shAHR (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117197 Embryonic brain of wild-type mice vs. luxoid mice
Contributors : Hsin-Chuan Lin ; Yung-Hao Ching ; Chi-Chen Huang ; Ping-Chieh Pao ; Yi-Hua Lee ; Wen-Chang Chang ; Tzu-Jen Kao ; Yi-Chao LeeSeries Type : Expression profiling by arrayOrganism : Mus musculusComparison of forebrain and midbrain from embryonic day 10.5 C57BL/6 wild-type mice and luxoid mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE117207 Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [Hi-C]
Contributors : Wei Tao ; YiTing Guan ; Chao ZhangSeries Type : OtherOrganism : Mus musculusThe emerging 4D genome project aiming to map the dynamics of genomes in spatial and temporal dimension has put forward to developing the mechanisms of how the nucleus is organized and functions. Therefore, processes like cellular senescence characterized by complex events give rise to understanding the regulation network from 1D genome to dynamically organized 3D structure. Unfortunately, how spatial genome reorganization triggers cellular senescence and how it influences senescence-related downstream transcriptional profile remains ...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE117208 Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [RNA-seq]
Contributors : Wei Tao ; YiTing Guan ; Chao ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe emerging 4D genome project aiming to map the dynamics of genomes in spatial and temporal dimension has put forward to developing the mechanisms of how the nucleus is organized and functions. Therefore, processes like cellular senescence characterized by complex events give rise to understanding the regulation network from 1D genome to dynamically organized 3D structure. Unfortunately, how spatial genome reorganization triggers cellular senescence and how it influences senescence-relate...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117209 Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile [ChIP-seq]
Contributors : Wei Tao ; YiTing Guan ; Chao ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe emerging 4D genome project aiming to map the dynamics of genomes in spatial and temporal dimension has put forward to developing the mechanisms of how the nucleus is organized and functions. Therefore, processes like cellular senescence characterized by complex events give rise to understanding the regulation network from 1D genome to dynamically organized 3D structure. Unfortunately, how spatial genome reorganization triggers cellular senescence and how it influences sen...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE117210 Architectural alterations in enhancer repertoires orchestrate senescence-associated secretory phenotype profile
Series Type : Other ; Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - July 18, 2018 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE117216 Paneth cells respond to inflammation and SCF/c-Kit signaling by acquiring stem-like features and contributing to tissue regeneration
Contributors : Riccardo R Fodde ; Mark M Schmitt ; Wesley W van de Geer ; Harmen H van de WerkenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe experiment aims to analyze the differences in expressed genes in Paneth cells upon acute intestinal inflammation compared to Paneth cells from non-inflamed control mice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117222 WDR-23 and SKN-1 Nrf2 coordinate with the BLI-3 dual oxidase in response to iodide-triggered oxidative stress
Contributors : Zhaofa Xu ; Long MaSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansExcess iodide could lead to larve arrest to C. elegans, we screened for mutants that can survive in excess iodide and identified gain-of-function mutations in skn-1 and loss-of-function mutations in wdr-23 and bli-3. Genetic study uncover that wdr-23(lf) can interact with bli-3 mutations in a manner different from skn-1(gf). Transcriptome studies suggest that excess iodide causes developmental arrest largely independent of changes in gene expression, and wdr-23(lf) could affect the expression o...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE117229 Metabolism regulates muscle stem cell self renewal by connecting the microenvironment and histone acetylation
Contributors : C H Ly ; Jennifer Trieu ; Shian Su ; Luyi Tian ; Daniela Zalcenstein ; Shalin H Naik ; Matthew E Ritchie ; Gordon S Lynch ; James G RyallSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSkeletal muscle contains a resident population of somatic stem cells capable of both self-renewal and differentiation. The signals that regulate this important decision have yet to be fully elucidated. Here we use single cell RNAseq to identify the innate metabolic signature of muscle stem cells. We show that committed muscle progenitor cells exhibit an enrichment of glycolytic and TCA cy...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117238 Transcriptome profiling identified a 3-lncRNA regulatory network in transthyretin against glucose induced hRECs dysfunction
Contributors : Jun Shao ; Yong YaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose (HG) or high glucose with 4 uM TTR (HG+TTR) were conducted. Differentially expressed lncRNAs, mRNAs and TTR related lncRNAs and mRNA were acquired for further analysis. Functional annotation and enrichment including KEGG pathway, GO and GSEA were applied to analyze TTR regulated pathway and process. WGCNA analysis was implemented to obtain hub modules and genes. LncRNA-mRNA regulatory network were constru...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117240 ATF4 couples MYC-dependent translational activity to bioenergetic demands during tumor progression
Contributors : Constantinos Koumenis ; Feven TameireSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDysregulation of the proto-oncogene c-Myc (MYC henceforward) drives malignant progression, but also induces robust anabolic and proliferative programs leading to intrinsic stress. The mechanisms enabling adaptation to MYC-induced stress are not fully understood. We have uncovered an essential role for the transcription factor ATF4 in cell survival following MYC activation. MYC- upregulates ATF4 by activating GCN2 kinase through uncharged tRNAs. Subsequently, ATF4 co-occupi...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117246 Structural, physiological and regulatory analysis of maltose transporter genes in Saccharomyces eubayanus CBS12357T.
Contributors : Jean-Marc Daran ; Marcel van den BroekSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces eubayanusSaccharomyces pastorianus lager brewing yeasts are domesticated hybrids of Saccharomyces cerevisiae and cold-tolerant Saccharomyces eubayanus. To better understand the contribution of both parental genomes to maltose metabolism in brewing wort, this study focuses on maltose transport in the S. eubayanus type strain CBS12357T/FM1318T. To obtain complete sequences of the MAL loci of this strain, a near-complete genome assembly was generated using the Oxford Nanopore Technology...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces eubayanus Source Type: research

GSE117247 Ruxolitinib inhibits Cyclosporine-induced proliferation of cutaneous squamous cell carcinoma
In this study, microarray data was used to compare normal skin to immunocompetent SCC, to transplant associated SCC (TSCC) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117249 Novel differences in renal gene expression in a diet-induced obesity model
Contributors : Victoria L Halperin Kuhns ; Jennifer L PluznickSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusObesity is a significant risk factor for both chronic kidney disease and end-stage renal disease. To better understand disease development, we sought to identify novel genes differentially expressed early in disease progression. We first confirmed that mice fed a high-fat (HF) diet exhibit early signs of renal injury including hyperfiltration. We then performed RNA-Seq using renal cortex RNA from C57BL6/J male mice fed either HF or control (Ctrl) diet. We identified 1,134 gene...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117251 Gene expression analysis in fly ovaries growing from somatic tkv-knockdown gonads driven by c587-GAL4
Contributors : Hweijan Hsu ; Cheng-Yuan TsengSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterPurpose: The goal of this study is to analyze genes affected by Tkv knockdown in the developing ovarian soma using RNA-seq.Ovarian mRNA prolife of one-day-old control flies and flies carring tkv-knockdown ovarian somatic cells duirng development by deep sequence, in duplicate, using Illumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript isoform level using TopHat followed by Cufflinks. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE117260 Developmental origins of neurotransmitter and transcriptome alterations in adult female zebrafish exposed to atrazine during embryogenesis
In this study, zebrafish embryos were exposed to 0, 0.3, 3, or 30 mg/L atrazine throughout embryogenesis. Larvae were then allowed to mature under normal laboratory conditions with no further chemical treatment until 7 days post fertilization (dpf) or adulthood and neurotransmitter analysis completed. No significant alterations in neurotransmitter levels was observed at 7 dpf or in adult males, but a significant decrease in 5-hydroxyindoleacetic acid (5-HIAA) and serotonin turnover was seen in adult female brain tissue. Transcriptomic analysis was completed on adult female brain tissue to identify molecular pathways underl...
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Danio rerio Source Type: research

GSE117265 Mapping of regions that are systematically under-replicated in metaphase, S. cerevisiae (2017-03-23)
Contributors : Tsvetomira Ivanova ; Alsu MissarovaSeries Type : Genome variation profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeWe establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE117266 Mapping of regions that are systematically under-replicated in metaphase and establishing the role of CDK-inhibition in accomplishing DNA-replication in these regions, S. cerevisiae (2017-09-15)
Contributors : Tsvetomira Ivanova ; Alsu MissarovaSeries Type : Genome variation profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeWe establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase. Inhibition of CDK activity, in fact, results in accomplishing of DNA replication in those regions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE117267 Mapping of regions that are systematically under-replicated in metaphase and telophase, S. cerevisiae (2017-10-06)
Contributors : Michael Maier ; Alsu MissarovaSeries Type : Genome variation profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeWe establish that subtelomeric regions together with some other functional elements like transposons are consistently under-replicated in metaphase and with lower extent in late anaphase, suggesting and ongoing DNA replication between metaphase and telophase. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 18, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE116157 Osterix functions downstream of anti-Mu ̈llerian hormone signaling to regulate Müllerian duct regression
Contributors : Rachel D Mullen ; Richard R BehringerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to identify potential AMH-induced genes and regulatory networks controlling regression by RNA-Seq transcriptome analysis of differences in M üllerian Duct mesenchyme between males (AMH signaling on) and females (AMH signaling off) in purified fetal Müllerian Duct mesenchymal cells. This analysis found 82 genes up-regulated in males during MD regression and identified Osterix (Osx)/Sp7, a key transcriptional regulator of osteoblast diff erentiation an...
Source: GEO: Gene Expression Omnibus - July 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE71345 Agilent zebrafish V3 array 4 ´44K microarray-Ochratoxin A treated with 6-48 hpf zebrafish embryos
In this study, the zebrafish was applied to investigate the effects of ochratoxin A on gene expressions in zebrafish embryos. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Danio rerio Source Type: research

GSE71346 Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6-48 hpf zebrafish embryos
Contributors : Biing-Hui Liu ; Ting-Shuan WuSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Danio rerioTo investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Danio rerio Source Type: research

GSE93272 Whole blood gene expression of rheumatoid arthritis
We report a longitudinal monitoring of the drug response at multi-omics levels in the peripheral blood of patients with RA. Our data reveal that drug treatments alter the molecular profile closer to that of HCs at the transcriptome, serum proteome and immunophenotype level. Patient follow-up suggests that the molecular profile after drug treatments is associated with long-term stable CR. In addition, we identify molecular signatures that are resistant to drug treatments. These signatures are associated with RA independently of known disease severity indexes and are largely explained by the imbalance of neutrophils, monocyt...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE93776 Immune cells gene expression from rheumatoid arthritis and healthy donors
We report a longitudinal monitoring of the drug response at multi-omics levels in the peripheral blood of patients with RA. Our data reveal that drug treatments alter the molecular profile closer to that of HCs at the transcriptome, serum proteome and immunophenotype level. Patient follow-up suggests that the molecular profile after drug treatments is associated with long-term stable CR. In addition, we identify molecular signatures that are resistant to drug treatments. These signatures are associated with RA independently of known disease severity indexes and are largely explained by the imbalance of neutrophils, monocyt...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE93777 Multi-omics monitoring of drug response in rheumatoid arthritis.
We report a longitudinal monitoring of the drug response at multi-omics levels in the peripheral blood of patients with RA. Our data reveal that drug treatments alter the molecular profile closer to that of HCs at the transcriptome, serum proteome and immunophenotype level. Patient follow-up suggests that the molecular profile after drug treatments is associated with long-term stable CR. In addition, we identify molecular signatures that are resistant to drug treatments. These signatures are associated with RA independently of known disease severity indexes and are largely explained by the imbalance of neutrophils, monocyt...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE94832 HDAC3-mediated regulation of the circadian gene Per1 contributes to age-related impairments in hippocampal memory and synaptic plasticity
Contributors : J L Kwapis ; M A Wood ; C N Magnan ; P F BaldiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed an RNA Sequencing experiment on dorsal hippocampal tissue from six groups of animals: Aging (18-20-month-old) HDAC3flox/flox homecage (H3F-HC); Aging (18-20-month-old) HDAC3flox/flox 60min post training (H3F-BV); Aging (18-20-month-old) wildtype homecage (OWT-HC); Aging (18-20-month-old) wildtype 60min post training (OWT-BV); Young (2-4-month-old) wildtype homecage (YWT-HC); Young (2-4-month-old) wildtype 60min post training (YWT-BV). Homecage animals were sacrific...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97613 Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth
Contributors : Yoseb Song ; Jongoh Shin ; Yujin Jeong ; Sangrak Jin ; Bong H Sung ; Dong R Kim ; Sun C Kim ; Suhyung Cho ; Byung-Kwan ChoSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Eubacterium limosumAutotrophic conversion of CO2 to value-added biochemicals has received considerable attention for the sustainable route to replace the fossil fuels. Particularly, anaerobic acetogenic bacteria are naturally capable of reducing CO2 or CO to various metabolites. To fully utilize their biosynthetic potential, systemic understanding of the metabolic network with the transcriptional and transl...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Eubacterium limosum Source Type: research

GSE106419 Gene expression analyses of mouse mesenchymal cells, keratinocytes and induced stratified epithelial progenitor cells.
We report the method for generating epithelial tissues from bottom of ulcer by lineage conversion. Both in vitro and in vitro, mesenchymal cells can be converted to the cells having ability to form stratified epithelium by transduction of lineage-specific transcription factors. We named the converted cells as induced stratified epithelial progenitor cells (iSEPs). Gene expression signatures of mesenchymal cells, in vitro generated iSEPs, in vivo generated iSEPs, and primary keratinocytes are analyzed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE107690 G-quadruplex structures moulds the DNA methylome
Contributors : Jochen Spiegel ; Avazeh Ghanbarian ; Giovanni Marsico ; Dario Beraldi ; Robert H änsel-Hertsch ; Shiqing Mao ; David Tannahill ; Shankar BalasubramanianSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensControl of DNA methylation level is critical for gene regulation, and the factors that govern hypomethylation at CpG islands (CGIs) are still being uncovered. Here, we provide evidence that G-quadruplex (G4) DNA secondary structures are genomic features that influence methylation at CGIs. We show that the presence of G4 structure is tightly associated wit...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109320 Regenerating hair cells in human vestibular sensory epithelia
Contributors : Anastasia Filia ; Michael LovettSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo investigate alterations in gene expression after Ad2-ATOH1-GFP transduction of human supporting cells, we measured transcriptome changes by RNA-seq. We compared gentamicin-treated tissue (to kill the hair cells) transduced with Ad2-ATOH1-GFP (to promote hair cell production) cultured for 5 days, versus control tissues only treated with gentamicin (cultured for 2 days, 8 days and 14-18 days). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110575 Persistence of DNA-RNA hybrids causes large genomic regions of aberrant DNA
Contributors : Lorenzo Costantino ; Douglas KoshlandSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeChromatin immuno-precipitation (ChIP) of Rad52-bound to ssDNA that was compatible with next-generation sequencing to map sites of DNA damage induced by accumulation of genomic DNA-RNA hybrids. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE110991 AAV9 mediated overexpression of Rbm24 in wildtype C57/Bl6 mice
Contributors : Maarten M van den Hoogenhof ; Esther E CreemersSeries Type : Expression profiling by arrayOrganism : Mus musculusThe RNA-binding protein Rbm24 has recently been identified as a pivotal splicing factor in the developing heart. Loss of Rbm24 in mice disrupts cardiac development by governing a large number of muscle- specific splicing events. Since Rbm24 knockout mice are embryonically lethal, the role of Rbm24 in the adult heart remained unexplored. Here, we used adeno-associated viruses (AAV9) to investigate the effect of increased Rbm24 levels in adult mouse heart. Using high-resolution microarrays, we found...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE111498 mRNA sequencing of live and encysting cells of Colpoda aspera
Contributor : Wei MiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Colpoda asperaThe goals of this study is to investigate the encystment mechanism. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Colpoda aspera Source Type: research

GSE112430 Comparative Transcriptome Profiling Reveals a Potential Role of Type VI Secretion System and Fimbriae in Virulence of Non-O157 Shiga Toxin-Producing Escherichia coli
Contributors : Christina G Ås ; Finn Drabløs ; Kjersti Haugum ; Jan E AfsetSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coliWe have used RNA sequencing to compare transcriptomes of 30 stx2a and eae positive STEC strains of non-O157 serogroups isolated from children
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Escherichia coli Source Type: research

GSE113911 mRNA sequencing of live and encysting cells of Colpoda aspera.
Contributor : Wei MiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Colpoda asperaThe goals of this study is to investigate the encystment mechanism. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Colpoda aspera Source Type: research

GSE114290 Genomic DNA sequencing of budding yeast strains
We report DNA content of yeast strains that are growing asynchronously or treated with hydroxyurea (HU). We selected two strains from our Epi-Decoder library, that are wild-type but have BAR1 or RPO21 TAP-tagged. This reveals that HU-treated samples have peaks in DNA content representing stalled replication forks. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE114406 ERRFI1 targeting by miR-205 mediates adaptive resistance to MET inhibition through enhanced EGFR signaling
Contributors : Cristina Migliore ; D Cor à ; Silvia GiordanoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe onset of secondary resistance represents a major limitation to long term efficacy of target therapies in cancer patients. Thus, the identification of mechanisms mediating secondary resistance is key to the rational design of alternative therapeutic strategies for resistant patients. MiRNA profiling combined with RNA-seq in MET-addicted gastric and lung cancer cell lines led us to identify the miR-205/ERRFI1 (ERBB receptor feedback inhibitor-1) axis as a novel mediator...
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115948 Identification of genes involved in GABAergic Wiring
Contributors : Antonio J Hinojosa ; Beatriz RicoSeries Type : Expression profiling by arrayOrganism : Mus musculusHow neurons are wired to form precise circuits is crucial to understand the development of cortical functions. Glutamatergic pyramidal cell and GABAergic interneuron wire up the cortex through differentiated cellular events. However, little is known about the molecular mechanisms that underlie the unique features of interneuron wiring.We performed a high-throughput genomic screen for genes upregulated specifically during GABAergic wiring. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research