GSE122728 RNASeq of C. elegans exposed to silver (Ag) or silicon dioxide (SiO2) nanoparticles
Contributors : Charles Viau ; Or çun Haçariz ; Jianguo XiaSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansRNAseq was carried out to compare the gene expression profiles underlying the Ag and SiO2 toxicities on C. elegans. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE67215 Fitness assay of Candida albicans strains grown in vitro or in vivo in a mouse model of gastrointestinal colonization
Contributor : Sadri ZnaidiSeries Type : OtherOrganism : Candida albicansCandida albicans is part of the human mycobiota, coexisting with the plethora of bacterial species within the gut. To better understand how C. albicans efficiently establishes gastrointestinal (GI)-tract colonization, we competitively challenged growth of 579 signature-tagged C. albicans strains (~ 10% genome coverage), each conditionally overexpressing a single gene, in the gut of a mouse model of GI-tract colonization. Our screen identified CRZ2, a transcription factor whose overexpression and deletion respectively increased and decreased early GI co...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Other Candida albicans Source Type: research

GSE67226 Genome-wide expression profiling of Candida albicans transcription factor Crz2p
Contributor : Sadri ZnaidiSeries Type : Expression profiling by arrayOrganism : Candida albicansCandida albicans is part of the human mycobiota, coexisting with the plethora of bacterial species within the gut. To better understand how C. albicans efficiently establishes gastrointestinal (GI)-tract colonization, we competitively challenged growth of 579 signature-tagged C. albicans strains (~ 10% genome coverage), each conditionally overexpressing a single gene, in the gut of a mouse model of GI-tract colonization. Our screen identified CRZ2, a transcription factor whose overexpression and deletion respectively increased a...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Candida albicans Source Type: research

GSE67233 Genome-wide location of Candida albicans transcription factor Crz2p
Contributor : Sadri ZnaidiSeries Type : Genome binding/occupancy profiling by genome tiling arrayOrganism : Candida albicansCandida albicans is part of the human mycobiota, coexisting with the plethora of bacterial species within the gut. To better understand how C. albicans efficiently establishes gastrointestinal (GI)-tract colonization, we competitively challenged growth of 579 signature-tagged C. albicans strains (~ 10% genome coverage), each conditionally overexpressing a single gene, in the gut of a mouse model of GI-tract colonization. Our screen identified CRZ2, a transcription factor whose overexpression and delet...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by genome tiling array Candida albicans Source Type: research

GSE67235 A Highly Parallel Conditional Overexpression Screen, in vivo, Provides New Insights into Candida albicans' Early Adaptation to the Mammalian Gut
Series Type : Other ; Expression profiling by array ; Genome binding/occupancy profiling by genome tiling arrayOrganism : Candida albicansThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Other Expression profiling by array Genome binding/occupancy profiling by genome tiling array Candida albicans Source Type: research

GSE85774 Choroid Plexus Gene Expression in ApoE3 or ApoE4-Knockin Mouse Choroid Plexuses
Contributors : Changjun Yin ; Andreas HabenichtSeries Type : Expression profiling by arrayOrganism : Mus musculusLaser capture microdissected choroid plexuses were obtained and expression arrays were generated to investigate gene expression in ApoE-Knockin choroid plexuses; the choroid plexus forms the cerebrospinal fluid, the cerebrospinal fliod barrier, functions as the major gateway for blood-born leukocytes to enter the brain in degenerative and inflammatory brain diseases, and the principal neuroimmune interface in the brain. We found lipid deposits in the aged choroid plexus of hyperlipidemic ApoE4-Knockin mice but n...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE85775 Choroid Plexus Gene Expression in wild-type (wt) and ApoE-deficient Mouse Choroid Plexuses
Contributors : Changjun Yin ; Andreas HabenichtSeries Type : Expression profiling by arrayOrganism : Mus musculusLaser capture microdissected choroid plexuses were obtained and expression arrays were generated to investigate gene expression in wt and ApoE choroid plexuses; the choroid plexus forms the cerebrospinal fluid, the cerebrospinal fliod barrier, functions as the major gateway for blood-born leukocytes to enter the brain in degenerative and inflammatory brain diseases, and the principal neuroimmune interface in the brain. We found lipid deposits in the aged choroid plexus of hyperlipidemic mice but none in the wt c...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE88894 TFEB controls vascular development by regulating the proliferation of endothelial cells (TFEB ChIp-seq)
Contributors : Gabriella Doronzo ; Elena Astanina ; Davide Cora' ; Francesco Neri ; Salvatore Oliviero ; Bussolino FedericoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe role of the transcription factor EB (TFEB) in the control of cellular functions, including in vascular bed, is mostly thought to be the regulation of lysosomal biogenesis and autophagic flux. While this is its best-known function, we report here the ability of TFEB to orchestrate a non-canonical program involved in the control of cell-cycle and VEGFR2 pathway in the developing vasculature. In endoth...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE88895 TFEB controls vascular development by regulating the proliferation of endothelial cells (sh-TFEB marray)
Contributors : G Doronzo ; D CoraSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe role of the transcription factor EB (TFEB) in the control of cellular functions, including in vascular bed, is mostly thought to be the regulation of lysosomal biogenesis and autophagic flux. While this is its best-known function, we report here the ability of TFEB to orchestrate a non-canonical program involved in the control of cell-cycle and VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB deletion halts proliferation by inhibiting the CDK4/Rb pathway, which regulates the cell cycle G1-S transit...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE88896 TFEB controls vascular development by regulating the proliferation of endothelial cells
Series Type : Expression profiling by array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe role of the transcription factor EB (TFEB) in the control of cellular functions, including in vascular bed, is mostly thought to be the regulation of lysosomal biogenesis and autophagic flux. While this is its best-known function, we report here the ability of TFEB to orchestrate a non-canonical program involved in the control of cell-cycle and VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB deletion halts proliferation by inhibiting the CDK4/Rb pathway, which reg...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE97943 Genome-wide expression profiling in bladder cancer cells
Contributors : Dimitrios Iliopoulos ; Marina KoutsioumpaSeries Type : Expression profiling by arrayOrganism : Homo sapiensDifferential gene expression profiling in PPP2R2A depleted RT-112 cells was performed using Human Genome U133 Plus 2.0 Array (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE100115 Time-course global miRNA expression profiling on lung fibroblasts isolated from untreated, bleomycin-treated and silica-treated mice
Contributors : Shin-ichi Hashimoto ; Shigeyuki Shichino ; Satoshi Ueha ; Kouji MatsushimaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusLung fibroblasts play a pivotal role in pulmonary fibrosis, a devastating lung diseases, by producing extracellular matrix. MicroRNAs (miRNAs) suppress a lot of genes posttranscriptionally, but the dynamics and the role of miRNAs in activated lung fibroblasts in fibrotic lung has been poorly understood. To elucidate these problems, we performed global miRNA expression profiling of lung fibroblasts of bleomycin- and silica-induced fibrotic lungs (...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE100116 Transcriptomic analysis of miR-19a-19b-20a subcluster-overexpressed fibroblasts in bleomycin-induced lung fibrosis
Contributors : Shigeyuki Shichino ; Shin-ichi Hashimoto ; Shungo Deshimaru ; Kunihiko Soma ; Satoshi Ueha ; Kouji MatsushimaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLung fibroblasts play a pivotal role in pulmonary fibrosis, a devastating lung diseases, by producing extracellular matrix. MicroRNAs (miRNAs) suppress a lot of genes posttranscriptionally, but the dynamics and the role of miRNAs in activated lung fibroblasts in fibrotic lung has been poorly understood. We found miR-19a, 19b and 20a subcluster expression increased in activated lung fibroblasts as the fibrosis progre...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100147 Global miRNA expression profiling of lung fibroblasts identifies miR-19a-19b-20a subcluster as a suppressor of TGF-beta-associated fibroblast activation in murine pulmonary fibrosis
Series Type : Non-coding RNA profiling by high throughput sequencing ; 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 - November 20, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE103217 Role of interleukin 2 on Foxp3+CD4+ regulatory T (Treg) cell gene expression and chromatin modeling in thymus and lymph node, and on SATB1 DNA binding in single positive CD4 thymocytes
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Mus musculusInterleukine 2 (IL-2) is still one of the most interesting cytokines in T cell biology with its ability to control immune homeostasis by maintaining the functional identity of Foxp3+ regulatory T (Treg) cells and the expansion of activated conventional T (Tconv) cells. Yet, how IL-2 exactly enables Treg cells to suppress autoreactive Tconv cells and to maintain their identity is unclear. Using a mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, t...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Mus musculus Source Type: research

GSE105148 A metabolic checkpoint controls hyphal development in Candida albicans via nitric oxide signaling
Contributors : Ana Traven ; Paul F Harrrison ; Traude H BeilharzSeries Type : Expression profiling by high throughput sequencingOrganism : Candida albicansWe investigated the roles of mitochondrial dynamics in hyphal growth of C. albicans using the small molecule inhibitor MDIVI-1. Strikingly, the small molecule inhibitor represses both the yeast-to hyphae transition and ongoing filamentation, and its effects on morphogenesis can be uncoupled from general growth inhibition. RNAseq experiments of inhibitor-treated cells coupled with Candida mutant analyses suggest the existence of a novel mechanism of action to represses hy...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Candida albicans Source Type: research

GSE106874 Combinatory RNA sequencing analyses reveal RNA editing-dependent and -independent gene regulation by ADAR1 in gastric cancer
Contributor : Charles J ChoSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensTo investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing were performed in AGS and MKN-45 cells with stable ADAR1 knock-down. Changed frequencies of editing and messenger RNA (mRNA) and microRNA (miRNA) expression were then identified by bioinformatic analyses. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107135 Effects of acid stress on gene transcription of L.lactis strain F44
Contributors : Kairen Tian ; Hao Wu ; Jianjun QiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Lactococcus lactisBacteria that live in the acidic environment face number of growth-related challenges from the intracellular pH changes. In order to survive under acidic environment, Lactic acid bacteria must employ multiple genes and proteins to regulate the relative pathways. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Lactococcus lactis Source Type: research

GSE107136 Effects of acid stress on gene transcription of L.lactis strain G423
Contributors : Kairen Tian ; Hao Wu ; Jianjun QiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Lactococcus lactisBacteria that live in the acidic environment face number of growth-related challenges from the intracellular pH changes. In order to survive under acidic environment, Lactic acid bacteria must employ multiple genes and proteins to regulate the relative pathways. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Lactococcus lactis Source Type: research

GSE107137 Transcriptome analysis of L.lactis F44 and G423: insights into adaptation to acidic environment
Series Type : Expression profiling by high throughput sequencingOrganism : Lactococcus lactisThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Lactococcus lactis Source Type: research

GSE107246 Identification of INSL4-regulated gene program in non-small cell lung cancer cells
Contributor : Lizi WuSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression profiling was performed to identify INSL4-regulated gene program in non-small cell lung cancer A549 cells. We compared gene expression profiles of A549 cells transduced with lentiviruses expressing scrambled shRNA control or INSL4 shRNA. Our analysis revealed INSL4-regulated gene program that are involved in the regulation of cell cycle, growth and survival. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107746 Transcriptome Landscape of Human Folliculogenesis Reveals Oocytes and Granulosa Cells Interactions
Contributors : Yaoyao Zhang ; Zhiqiang Yan ; Jie QiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe dynamic transcriptional regulation and interactions of human germlines and surrounding somatic cells during folliculogenesis remains unknown. Using RNA-Seq analysis of human oocytes and corresponding granulosa cells (GCs) spanning five follicular stages, we revealed unique features in transcriptional machinery, transcription factor networks and reciprocal interactions in human oocytes and GCs that displayed developmental-stage-specific expression patterns. Notably, we identified sp...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107858 Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (MCF7)
In this study, we performed single-cell transcriptome analysis on ERα-positive breast cancer cell lines following 17β-estradiol stimulation. We sequenced a total of 177 single-cell transcriptomes and observed robust gene expression diversity between individual cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107863 Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells (T47D)
In this study, we performed single-cell transcriptome analysis on ERα-positive breast cancer cell lines following 17β-estradiol stimulation. We sequenced a total of 177 single-cell transcriptomes and observed robust gene expression diversity between individual cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107864 Single-cell transcriptome analysis reveals estrogen signaling augments the mitochondrial folate pathway to coordinately fuel purine and polyamine synthesis in breast cancer cells
Contributors : Detu Zhu ; Xianglan Zhaozu ; Edwin CheungSeries 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 - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107952 Identifying lncRNA-MM2P as a novel modulator of macrophage M2 polarization
Contributors : Ji Cao ; Rong DongSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Mus musculusBy utilizing a series of specific modulating M2 macrophages polarization models, 1556 up-regulated and 953 down-regulated genes were found during the polarization process. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Mus musculus Source Type: research

GSE107979 Identifying lncRNAs as novel modulators of macrophage M2 polarization
Contributors : Ji Cao ; Rong DongSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Mus musculusBy utilizing a series of specific modulating M2 macrophages polarization models, 3872 up-regulated and 3091 down-regulated genes were found during the polarization process. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Mus musculus Source Type: research

GSE108503 Pathway analysis of RNA sequencing of various stages of myodifferentiation identifies conditions favoring type I and type II fibers, and highlights increased efficiency of combined differentiation
Contributors : Alexander V Predeus ; Oksana A Ivanova ; Natalia V Khromova ; Artem M Kiselev ; Dmitry E Polev ; Natalia A Smolina ; Anna A Kostareva ; Renata I DmitrievaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA-Seq of C2C12 cells differentiated for 0, 2, or 7 days using classic myogenic (DM1), adipogenic (DM2), or mixed (DM3) stimulation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE109457 Transcriptional changes of serum stimulation in mouse embryonic fibroblasts due to loss of PIN1
Contributors : Rosalie Sears ; Yulong SuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to determine the transcriptional difference between WT and PIN1 knockout mouse embryonic fibroblasts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE109458 Effect of global MYC DNA binding due to loss of PIN1
Contributors : Rosalie Sears ; Yulong SuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to determine the MYC binding difference between WT and PIN1 knockout mouse embryonic fibroblasts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE109459 Post-translational modification of MYC localizes MYC to the nuclear pore basket to regulate local histone acetylation and gene expression
Series Type : 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 - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE109958 Transcriptome reprogramming at late stage of desiccation defines the resurrection behavior of Haberlea rhodopensis
Contributors : Xu Tao ; Chih-Ta LinSeries Type : Expression profiling by high throughput sequencingOrganism : Haberlea rhodopensisWater shortage is a major factor that harms agriculture and ecosystems worldwide. Plants display various levels of tolerance to water deficit, but only resurrection plants can survive full desiccation of their vegetative tissues. Haberlea rhodopensis, an endemic plant of the Balkans, is one of the few resurrection plants found in Europe. We performed transcriptomic analyses of this species under slight, severe and full dehydration and recovery to investigate the dynamics of gene expression and a...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Haberlea rhodopensis Source Type: research

GSE111474 Distinct constitutive and pathogen-induced transcriptional programs in dendritic cells derived from CD16- versus CD16+ monocytes
Contributors : Vanessa S Wacleche ; Jean-Philippe Goulet ; Am élie Cattin ; Dominique Gauchat ; Annie Gosselin ; Aurélie Cleret-Buhot ; Yuwei Zhang ; Cécile Tremblay ; Jean-Pierre Routy ; Petronela AncutaSeries Type : Expression profiling by arrayOrganism : Homo sapiensClassical CD16- versus intermediate/non-classical CD16+ monocytes differ in their homing potential and immunological functions; but whether they differentiate into dendritic cells (DC) with distinct contributions to immunity against bacterial/viral pathogens remains poorly investigated. Here, we employed a systems biology approach to ide...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112502 Regulatory Discrimination of mRNAs by FMRP Controls Adult Neural Stem Cell Differentiation
Contributors : Botao Liu ; Yue Li ; Emily E Stackpole ; Xinyu Zhao ; Joel D RichterSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusFragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), a translation-inhibitor RNA binding protein. The impact of FMRP-deficiency on neural function is widespread, including its regulation of adult neural stem cell (aNSC) differentiation. To assess FMRP activity, we performed ribosome profiling of aNSCs from normal and Fmr1 knockout mice, which revealed diverse gene expression changes at the mRNA and translat...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE113734 Loss of the Chr16p11.2 candidate gene QPRT leads to aberrant neuronal differentiation
Conclusions: In this study QPRT was causally related to in vitro neuronal differentiation and affected the regulation of genes and gene-networks that were previously implicated in ASD. Thus, our data suggest that QPRT may play an important role in the pathogenesis of ASD in Chr16p11.2 deletion carriers. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115167 Transcriptome Profiling of Japanese Encephalitis Virus (JEV) Infected Human Neuroepithelioma Cells (SK-N-MC)
This study, therefore, utilized the Affymetrix Human PrimeView array for a robust profiling of JEV infected SK-N-MC cells during the active phase of infection in order to investigate the molecular details of the host cell responses. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE115401 Impaired immune surveillance accelerates accumulation of senescent cells and aging [RNA-seq]
Contributors : Yossi Ovadya ; Tomer Landsberger ; Hanna Leins ; Ezra Vadai ; Hilah Gal ; Anat Biran ; Reut Yosef ; Adi Sagiv ; Amit Agrawal ; Alon Shapira ; Joseph Windheim ; Michael Tsoory ; Reinhold Schirmbeck ; Amit Ido ; Hartmut Geiger ; Valery KrizhanovskySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCellular senescence is a stress response that imposes stable cell-cycle arrest in damaged cells, preventing their propagation in tissues. However, long-term presence of senescent cells might promote tissue degeneration and malignant transformation via secreted pro-inflammatory and ...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE115771 Response of ECF sigma factor deletion mutants of Cupriavidus metallidurans to mixed metal ions (Co, Cu, Cd, Zn, Ni, 30 µM each)
Contributors : Cornelia Grosse ; Frank Reith ; Dietrich H NiesSeries Type : Expression profiling by arrayOrganism : Cupriavidus metallidurans ; Cupriavidus metallidurans CH34Response of Cupriavidus metallidurans CH34 and ECF deletion mutants to mixed metals (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Cupriavidus metallidurans Cupriavidus metallidurans CH34 Source Type: research

GSE116187 Homolog-selective degradation as a strategy to probe the function of CDK6 in AML
Contributors : Georg E Winter ; Matthias BrandSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe design of selective small-molecules is often stymied by similar ligand binding pockets. Here we report the first cyclin-dependent kinase 6 (CDK6) degrader, BSJ-03-123, that uses phthalimide-conjugation to exploit protein-interface determinants to achieve proteome-wide degradation selectivity. Pharmacologic CDK6 degradation targets a selective dependency of acute myeloid leukemia cells, and coupling acute degradation with transcriptomics and phosphoproteomics enabled dynamic mapping of the...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116593 Genome wide transcriptome analysis reveals complex regulatory mechanisms underlying phosphate homeostasis in soybean nodules
In this study, genome wide transcriptome analysis was conducted using RNA-seq analysis to investigate molecular mechanisms underlying soybean (Glycine max) nodule adaptation to phosphate (Pi) starvation. Phosphorus deficiency significantly decreased soybean nodule growth and nitrogenase activity. Nodule Pi concentrations declined by 49% in response to P deficiency, but this was well below the 87% and 88% decreases observed in shoots and roots, respectively. Nodule transcript profiling revealed that a total of 2,055 genes exhibited differential expression patterns between Pi sufficient and deficient conditions. A set of DEG...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Glycine max Source Type: research

GSE116681 Gene expression profiling shows that a jaz decuple mutation (jazD) promotes expression of defense-related genes while inhibiting expression of growth-related genes
Contributors : Qiang Guo ; Gregg A HoweSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThe decuple jaz mutation (jazD) affects plant growth and defense. We used RNA-sequencing to query the transcriptomes of a jaz quintuple mutant (jazQ) and jazD, and examined how these mutations alter the expression of growth- and defense-associated genes in comparison to wild-type Col-0 plants. The data highlight how jasmonate pathways contribute to growth and defense. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE116761 Pan-senescence transcriptome analysis identified RRAD as a marker and negative regulator of cellular senescence
Contributors : Zhao Wei ; Haiyang Guo ; Junchao Qin ; Qiao Liu ; Xiyu Zhang ; Yaoqin Gong ; Changshun ShaoSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensCellular senescence, an irreversible proliferative arrest, functions in tissue remodeling during development and is implicated in multiple aging-associated diseases. While senescent cells often manifest an array of senescence-associated phenotypes, such as cell cycle arrest, altered heterochromatin architecture, reprogrammed metabolism and senescence-associated secretory phenotype(SASP), the identification of senescenc...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE116827 Comparative transcriptomics of tomato plants simultaneously infested with different species of herbivorous mites reveals distinct signatures of host defense suppression
Contributors : B C Schimmel ; J M Alba ; J J Glas ; N Wybouw ; T T Meijer ; R C Schuurink ; M R KantSeries Type : Expression profiling by arrayOrganism : Solanum lycopersicumTomato plants are commonly attacked by herbivorous mites, including by generalist Tetranychus urticae and specialists Tetranychus evansi and Aculops lycopersici. Mite feeding induces plant defense responses that reduce mite performance. However, via poorly understood mechanisms, T. evansi and A. lycopersici suppress plant defenses and, consequently, maintain a high performance on tomato. Accordingly, on a shared host, non-adapted T. urticae can be faci...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Solanum lycopersicum Source Type: research

GSE117175 Rational engineering of Corynebacterium glutamicum for the production of the dicarboxylic acid glutarate
Contributors : Fernando P érez-García ; João P Jorge ; Annika Dreyszas ; Joe M Risse ; Volker F WendischSeries Type : Expression profiling by arrayOrganism : Corynebacterium glutamicum ; Corynebacterium glutamicum ATCC 13032The dicarboxylic acid glutarate is gaining attention in the chemical and pharmaceutical industry as promising building-block. Synthesis of glutarate via microbial fermentation is a desirable aim which will allow the production of biopolymers avoiding fossil raw materials. Here, by rational metabolic engineering of the biofactory microorganism Corynebacterium glutamicum the fermentat...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Corynebacterium glutamicum Corynebacterium glutamicum ATCC 13032 Source Type: research

GSE117488 Requirement for NF-kB in maintenance of molecular and behavioral circadian rhythms in mice.
Conclusions: Our findings cast new light on NF-kB as a pivotal genomic control node integrating metabolic inflammation and circadian systems at both the cellular and organismal levels. In particular, NF-kB directly regulates the expression of the negative limb of the clock while at the same time the clock activator TFs CLOCK/BMAL1 co-localize with NF-kB at new sites to regulate transcription following inflammatory stimuli. In addition, our data indicate significant overlap between NF-kB activation following both acute and chronic inflammatory challenges in liver. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE117752 Enhanced PAT-ChIP (EPAT-ChIP), a new procedure for reliable genome-wide studies in clinical FFPE tissues
Contributors : Stefano Amatori ; Giuseppe Persico ; Claudio Paolicelli ; Roman Hillje ; Nora Sahnane ; Francesco Corini ; Daniela Furlan ; Lucilla Luzi ; Saverio Minucci ; Marco Giorgio ; Pier Giuseppe Pelicci ; Mirco FanelliSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChromatin immunoprecipitation (ChIP) has allowed the study of protein-DNA interactions in chromatin, bringing new insights into the role of histone post-translational modifications (HPTMs) in cancer and other diseases. The coupling of ChIP with next-generation sequencing (NGS) techniques has revealed th...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117909 Targets and genomic constraints of ectopic Dnmt3b expression
Contributors : Yingying Zhang ; Jocelyn Charlton ; Rahul Karnik ; Isabel Beerman ; Zachary D Smith ; Hongcang Gu ; Patrick Boyle ; Kendell Clement ; Ramona Pop ; Andreas Gnirke ; Derrick J Rossi ; Alexander MeissnerSeries Type : Methylation profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusDNA methylation plays an essential role in mammalian genomes, hence DNA methyltransferase expression is tightly controlled. Deregulation of the de novo enzyme DNMT3B is frequently observed in many diseases, ...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE118157 Effects of rFVIIIFc on human macrophages
Contributor : Katalin Kis-TothSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensImmune responses in hemophilia A patients to replacement factor VIII can be either tolerogenic or immunogenic, the latter resulting in induction of non-neutralizing anti-factor VIII antibodies or neutralizing antibodies called inhibitors. Since these inhibitors render replacement FVIII treatment essentially ineffective, preventing or eliminating them are of top priority in disease management. The extended half-life recombinant factor VIII Fc fusion protein (rFVIIIFc) is an approved therapy for hemophilia A p...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118228 Gene expression data from human endometrial cancer cells treated with siRNA targeting Efp
Contributors : Wataru Sato ; Kazuhiro Ikeda ; Kuniko Horie-Inoue ; Satoshi InoueSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo examine the role of Efp in endometrial cancer cells, Ishikawa and HEC-1A cells were treated with siRNA targeting Efp (siEfp) or control siRNA (siControl). Microarray analysis showed that Efp knockdown represses NF- κB-signaling pathway-associated genes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE118766 Activation of a novel ULK1-MLK3-ERK5 pathway by the IFNg receptor is required for IFNg-inducible antiviral responses
Contributors : Diana Saleiro ; Patrick A Ozark ; Leonidas C PlataniasSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlthough well established that signal transducer and activator of transcription 1 (STAT1) activation is required for an interferon (IFN) -mediated antiviral response, the potential roles of other IFNg-activated cellular pathways in the process are unknown. We provide evidence that Unc-51-like kinase 1 (ULK1) is activated during engagement of the Type II IFN receptor and is required for IFNg-mediated transcription of key interferon stimulated genes involved in anti-vi...
Source: GEO: Gene Expression Omnibus - November 20, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research