GSE99782 Adenosine DeAminase-1 (ADA-1) improves Follicular helper T cell function and vaccine response
Series Type : Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104232 NFIA enables the rapid derivation of functional, human astrocytes from pluripotent stem cells by modulating G1 cell cycle length
Contributors : Lorenz Studer ; Jason TchieuSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe development of the central nervous system (CNS) depends on the orchestrated generation of neurons and glia from neural stem cells (NSCs). Although NSCs generate both cell types, they are produced sequentially as neurons are born first and glia later. In humans, this timing is extremely protracted and the underlying mechanisms remain unknown. Deriving glial cells such as astrocytes from human pluripotent stem cells requires 3-...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104585 Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis
In this study we investigated the molecular role of cytosine modification in the developing cortex of mice. To this aim we isolated thee linage related cell populations of the developing cortex and mapped both, 5mC as well as 5hmC on a genome-wide scale. Furthermore we established a system to site-specifcally demethylate DNA by using a dCas9-Tet1 fusion protein.Methods: Neuronal stem cells (Btg2-/Tubb3-), neurogenic progenitors (Btg2+/Tubb3-) and neurons (Tubb3+) were isolated from E14.5 Btg2-RFP/Tubb3-GFP double heterozygous mouse embryos (Aprea et al. 2013) and were used for a comparative immunoprecipitation of 5mC and 5...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE110027 Distinct gene expression changes in human peripheral blood mononuclear cells treated with different tobacco product preparations
Contributors : Quynh T Tran ; G L PrasadSeries Type : Expression profiling by arrayOrganism : Homo sapiensCigarette smoking exerts diverse physiological effects including immune suppression. Existing US epidemiological data show that consumption of smokeless tobacco products, such as moist snuff, is less harmful relative to cigarette smoking. In efforts to understand the molecular changes due to consumption of different tobacco product classes, we have shown recently that smokers exhibit distinct peripheral blood mononuclear cells (PBMCs) gene expression patterns relative to moist snuff users and non-tobacco consumers (NTC...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111079 Characterization of murine hepatoma cells with regard to their dependence on cyclin E1
Contributors : Roland Sonntag ; Nives Giebeler ; Yulia A Nevzorova ; J örg-Martin Bangen ; Dirk Fahrenkamp ; Daniela Lambertz ; Ute Haas ; Wei Hu ; Nikolaus Gassler ; Francisco J Cubero ; Gerhard Müller-Newen ; Ali T Abdallah ; Ralf Weiskirchen ; Fabio Ticconi ; Ivan G Costa ; Mariano Barbacid ; Christian Trautwein ; Christian LiedtkeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn C57BL/6 mice with a floxed cyclin E1 (CcnE1) gene (CcnE1f/f), hepatocellular carcinomas were induced using diethylnitrosamine (DEN). Hepatocyte-derived cells from pre-cancerous but tumor-free li...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111303 Expression data from sorted mouse postnatal day 2 lung alveolar type 2 cells
Contributor : Emma RawlinsSeries Type : Expression profiling by arrayOrganism : Mus musculusWe purified the differentiating alveolar type 2 cells from postnatal day 2 mouse lungs and used Affymetrix microarrays to obtain their gene expression profiles. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE111364 Transcriptome of microbiome for the nematode Caenorhabditis elegans
Contributors : Carola Petersen ; Barbara Pees ; Katja Dierking ; Hinrich SchulenburgSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansHost-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm ’s natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we charact...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE114558 Targeting an RNA-binding Protein Splicing Network in Acute Myeloid Leukemia
Contributors : Eric Wang ; Alessandro Pastore ; Sydney X Lu ; Xufeng Chen ; Jochen Imig ; Yohana E Ghebrechristos ; Akihide Yoshimi ; Lillian Bitner ; Andreas Kloetgen ; Kuan-Ting Lin ; Taisuke Uehara ; Takashi Owa ; Raoul Tibes ; Adrian R Krainer ; Omar Abdel-Wahab ; Iannis AifantisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-binding proteins (RBPs) are essential modulators of transcription and translation and are often dysregulated in cancer. Here we systematically interrogated RBP vulnerabilities in acute myeloid leukemia (AML) by performing a comprehensive CRISPR/Cas9 scree...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114979 The effect of colorectal cancer (CRC) organoid-derived extracellular vesicles on the expression profile of fibroblasts
Contributor : Zoltan WienerSeries Type : Expression profiling by arrayOrganism : Homo sapiensExtracellular vesicles (EV) are membrane-surrounded vesicles secreted by cells that carry biologically important molecules to the target cells. EVs form a heterogenous group and they represent a novel way of intercellular communication. To study the importance of colorectal cancer (CRC)-derived EVs on stromal fibroblasts, we applied CRC patient-derived 3D organoid cultures and commercially available human colon fibroblasts. We studied the gene expression changes in fibroblasts in the presence and absence pf CRC-derived EVs. (Source...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117189 Fisetin induces autophagy in pancreatic cancer cells via endoplasmic reticulum stress- and mitochondrial stress-dependent pathways
Contributors : S Jia ; X Xu ; S Zhou ; Y Chen ; G Ding ; L CaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPancreatic cancer is one of the most aggressive tumors and has poor survival rates. Fisetin, a natural flavonoid, was recently reported to have antitumor effects in various cancer models. Autophagy is a conserved catabolic process that maintains cellular homoeostasis in response to stress, and together with apoptosis, determines cell fate. Herein, we examined the effect of fisetin on pancreatic cancer. We reveal that fisetin inhibits Panc-1 cell proliferation in vivo and in vi...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117193 The induction of core pluripotency master regulators in cancers defines poor clinical outcomes and treatment resistance
Contributors : Anastasia Hepburn ; Rebecca E Steele ; Rajan Veeratterapillay ; Laura Wilson ; Amy Barnard ; Philip Berry ; James Cassidy ; Mohammad Moad ; Amira El-Sherif ; Luke Gaughan ; Ian G Mills ; Craig Robson ; Rakesh HeerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensClinical expression of core pluripotent stem cell master regulators OCT4, SOX2 and NANOG is associated with treatment resistance and lethal cancers. We have described a novel model to induce the expression of these factors in vitro. We term this culture environment ‘Acquired Pluripotent Stem Cell Environment...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117961 RNA-seq datasets for "A neuron-optimized CRISPR/dCas9 activation system for robust and specific gene regulation"
Contributors : Katherine E Savell ; Svitlana V Bach ; Morgan E Zipperly ; Jasmin S Revanna ; Nicholas A Goska ; Jennifer J Tuscher ; Corey G Duke ; Faraz A Sultan ; Julia N Burke ; Derek Williams ; Lara Ianov ; Jeremy J DaySeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusThis dataset contains whole-genome RNA sequencing results from rat embryonic hippocampal neuronal cultures and serves as the basis for characterization of CRISPR/dCas9 gene activation in neuronal systems. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE119271 A diffusion-based microfluidic device for single-cell RNA-seq
Contributors : Mimosa Sarma ; Chang LuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusMicrofluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-Seq). Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one microfluidic chamber. MID-RNA-Seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device de...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE119454 Assembly and functionality of the ribosome with tethered subunits
Contributors : Nikolay A Aleksashin ; Margus Leppik ; Adam J Hockenberry ; Dorota Klepacki ; Nora V ázquez-Laslop ; Michael C Jewett ; Jaanus Remme ; Alexander S MankinSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Escherichia coliRibo-T is an engineered ribosome whose small and large subunits are tethered together by insertion of circularly permutated 23S rRNA into 16S rRNA [Orelle, C., Carlson, E. D., Szal, T., Florin, T., Jewett, M. C., Mankin, A.S. Protein synthesis by ribosomes with tethered subunits. Nature 524, 119-124 (2015)]. Whether the growth defects are related to prob...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Escherichia coli Source Type: research

GSE122238 FTSEC cells (FT190 and FT194 cell lines) transduced with shRNA to knockdown RNF20 or with control shRNA
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE123495 Malaria Host Pathogen Interaction Center Experiment 30: Pilot experiment for Macaca mulatta infected with Plasmodium knowlesi Malayan strain sporozoites to produce and integrate measures of acute primary infection.
Contributors : John W Barnwell ; Steven E Bosinger ; Monica Cabrera-Mora ; Regina J Cordy ; Jeremy D DeBarry ; Mary R Galinski ; Allison Hankus ; Jay C Humphrey ; Nicolas Lackman ; Stacey A Lapp ; Alberto Moreno ; Mustafa Nural ; Suman B Pakala ; Nirav Patel ; Chester J Joyner ; Mariko S Peterson ; Gregory K TharpSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca mulatta ; Plasmodium knowlesiThis project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN27220120003...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Macaca mulatta Plasmodium knowlesi Source Type: research

GSE123714 Molecular features of PDGFRa+ mesenchymal progenitors and progeny in the mammary gland
Contributors : Purna A Joshi ; Katayoon Kasaian ; Rama Khokha ; Paul C BoutrosSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNA-seq on FACS-purified GFP+ and tdTomato+ stromal and luminal mammary populations from untreated and hormone stimulated adult PdgfraCreR26mTmG lineage tracing mice. Unsupervised hierarchical clustering of the top 20% most variable genes resulted in clustering of GFP+ and tdTomato+ stromal subsets into distinct groups. Distance-analysis of DEGs between GFP+ and tdTomato+ fractions in stromal and luminal lineages showed GFP+ stromal cells to have m...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125580  wMelpop strain of Wolbachia infection of Aedes albopictus mosquito C6/36 cells modulates dengue virus-induced host cellular transcripts and induces critical sequence alterations in dengue viral genome 
Contributors : Tadahisa Teramoto ; Xin Huang ; I ñaki Iturbe-Ormaetxe ; Scott L O’Neill ; Peter Armbruster ; Radhakrishnan PadmanabhanSeries Type : Expression profiling by high throughput sequencingOrganism : Aedes albopictusThe dengue virus (DENV) cause frequent epidemics infecting ~390 million people annually in over 100 countries. There are no approved vaccines or antiviral drugs for treatment of infected patients. However, there is a novel approach to control transmission of DENV by the mosquito vectors, Aedes aegypti and Ae. albopictus, using Wolbachia symbiont. The wMelPop strain of Wolbachia suppresses ...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Aedes albopictus Source Type: research

GSE126158 COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [DF]
Contributors : Yu Zheng ; Valentine Comaills ; Risa Burr ; Gaylor Boulay ; David T Miyamoto ; Ben S Wittner ; Erin Emmons ; Srinjoy Sil ; Michael W Koulopoulos ; Katherine T Broderick ; Eric Tai ; Shruthi Rengarajan ; Anupriya Kulkarni ; Toshi Shioda ; Chin-Lee Wu ; Sridhar Ramaswamy ; David T Ting ; Mehmet Toner ; Miguel Rivera ; Shyamala Maheswaran ; Daniel A HaberSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single cell RNA-sequen...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE126159 COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [CE1-4]
Contributors : Yu Zheng ; Valentine Comaills ; Risa Burr ; Gaylor Boulay ; David T Miyamoto ; Ben S Wittner ; Erin Emmons ; Srinjoy Sil ; Michael W Koulopoulos ; Katherine T Broderick ; Eric Tai ; Shruthi Rengarajan ; Anupriya Kulkarni ; Toshi Shioda ; Chin-Lee Wu ; Sridhar Ramaswamy ; David T Ting ; Mehmet Toner ; Miguel Rivera ; Shyamala Maheswaran ; Daniel A HaberSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTumor-stromal communication within the microenvironment contributes to initiation of metastasis and may present a therapeutic opportunity. Using serial single cell RNA-sequen...
Source: GEO: Gene Expression Omnibus - February 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE107439 Bifidobacterium kashiwanohense expresses fucosidases necessary for fucosyllactose utilisation as an adaptation to the infant gut environment
In this study, we read and annotate the full genome sequence of this novel strain, and use the data obtained to direct our further experimental analysis of fucosyllactose metabolism in B. kashiwanohense. Using transcriptomic and growth analysis results, we identify the genes responsible for B. kashiwanohense to utilise fucosyllactose, and employ a combination of cloning, in vitro hydrolysis assays, and further, recombinant transcriptomic and growth assays to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense, as well as revealing insight into fucosyllactose and fucose metabolism in Bifidobacteria as w...
Source: GEO: Gene Expression Omnibus - February 24, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Bifidobacterium breve UCC2003 Bifidobacterium kashiwanohense Source Type: research

GSE78267 Altered cell signaling in the absence of Dynamin function: a transcriptomic approach from yeast to humans (yeast)
Contributors : Macarena Morillo-Huesca ; Maria S Dominguez-Sanchez ; Tatiana Alfonso-Perez ; Monica Perez-Alegre ; Eloisa Andujar ; Valentina Bachetti ; Mario Garcia-Dominguez ; Jose C ReyesSeries Type : Expression profiling by arrayOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeDynamins are large multidomain GTPases involved in membrane scission. We have investigated the transcriptional consequences of deleting Vps1, a DNM2 homologue, in the yeast Saccharomyces cerevisiae. Interestingly, the vps1 ∆ mutation causes strong transcriptional defects also in yeast.Data suggest that DNM2 and Vps1 play an essent...
Source: GEO: Gene Expression Omnibus - February 24, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Saccharomyces cerevisiae Schizosaccharomyces pombe Source Type: research

GSE78269 Altered cell signaling in the absence of Dynamin function: a transcriptomic approach from yeast to humans (human)
Contributors : Maria S Dominguez-Sanchez ; Tatiana Alfonso-Perez ; Macarena Morillo-Huesca ; Monica Perez-Alegre ; E Andujar ; V Bachetti ; Mario Garcia-Dominguez ; C ReyesSeries Type : Expression profiling by arrayOrganism : Homo sapiensDynamins are large multidomain GTPases involved in membrane scission. We have investigated the transcriptional consequences of deleting DNM2 by siRNA in HeLa cells. Interestingly, DNM2 depletion causes strong transcriptional defects.Data suggest that DNM2 playes an essential regulatory role connecting several membrane-related processes including endocytosis, lipid homeostasis and different...
Source: GEO: Gene Expression Omnibus - February 24, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE126908 Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods [5 Cell Lines Cel-seq]
Contributors : Luyi Tian ; Daniela Amann-Zalcenstein ; Matthew E Ritchie ; Shian SuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle cell RNA sequencing (scRNA-seq) technology has undergone rapid development in recent years and brings new challenges in data processing and analysis. This has led to an explosion of tailored analysis methods for scRNA-seq to address various biological questions. However, the current lack of gold-standard benchmarking datasets makes it difficult for researchers to evaluate the performance of the many methods available in a systematic manner. Here, we...
Source: GEO: Gene Expression Omnibus - February 23, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE44977 Expression data from the mouse liver with constitutively active FoxO3
Contributors : Karlheinz Holzmann ; Sarah Gul ; Pavel Strnad ; Yoshiaki Sunami ; Thomas WirthSeries Type : Expression profiling by arrayOrganism : Mus musculusActivation of hepatic FoxO3 signaling induces hyperglycemia and hyperinsulinemia. Metformin administration reverses FoxO3-induced phenotype development.To investigate the underlying mechanism, we used microarrays to detail the global programme of gene expression which is regulated by hepatic FoxO3 signaling. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE66848 ADAMTSL2, a missing link in Wnt/ ß-catenin regulated CNS vascular development
In conclusion, the studies presented here reveal a hitherto unrecognized role of ADAMTSL2 as an endothelial cell-specific mediator of Wnt/ß-catenin signaling during CNS vascular development and BBB-formation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE95534 Gene knockdown in malaria parasites via non-canonical RNAi
Contributors : Franziska Hentzschel ; Sabine Fraschka ; Richard Bartf ái ; Ann-Kristin Mueller ; Dirk GrimmSeries Type : Expression profiling by high throughput sequencingOrganism : Plasmodium bergheiTo introduce a non-canonical RNA interference pathway into Plasmodium berghei (P. berghei), we generated a P. berghei line constitutively expressing the human protein Argonaute 2 (Ago2) and episomally expressed Ago2-dependent short hairpin RNAs (AgoshRNAs) against GFP. Using RNA sequencing (RNA-Seq), we analyzed transcriptomes of wild type parasites (PbGFPcon), Ago2-expressing parasites (PbAgo2) and PbAgo2 parasites exp...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Plasmodium berghei Source Type: research

GSE103781 Stroke target identification guided by astrocyte transcriptome analysis [pool]
Contributors : Cordula Rakers ; Melvin Schleif ; Thomas Ulas ; Kristian H ändler ; Santiago ValleTorres ; Toni Schumacher ; Khalid Tai ; Caroline Dalmoro ; Joachim L Schultze ; Walker Jackson ; Gabor C PetzoldSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusWe aimed to investigate the influence of ischemic stroke in mice on their ribosomal mRNA in astrocytes. Therefore, we make use of the conditional Cre/LoxP System in the RiboTag mouse line in order to isolate the ribosomal mRNA of astrocytes. CreERT2 expression under the astrocyte-specific Cx43 promoter is induced by Tam...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE103782 Stroke target identification guided by astrocyte transcriptome analysis [single animal]
Contributors : Cordula Rakers ; Melvin Schleif ; Thomas Ulas ; Kristian H ändler ; Santiago ValleTorres ; Toni Schumacher ; Khalid Tai ; Caroline Dalmoro ; Joachim L Schultze ; Walker Jackson ; Gabor C PetzoldSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusWe aimed to investigate the influence of ischemic stroke in mice on their ribosomal mRNA in astrocytes. Therefore, we make use of the conditional Cre/LoxP System in the RiboTag mouse line in order to isolate the ribosomal mRNA of astrocytes. CreERT2 expression under the astrocyte-specific Cx43 promoter is induced by Tam...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE103783 Stroke target identification guided by astrocyte transcriptome analysis
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE110970 Malaria Host Pathogen Interaction Center Experiment S01: Host and parasite gene transcript abundances, from cultured cells, of Macaca mulatta infected with Plasmodium knowlesi Pk1(A+), Pk1(B+)1+, Pk1(C+) ex vivo time course.
Contributors : Steven E Bosinger ; Jeremy D DeBarry ; Mary R Galinski ; Allison Hankus ; Jessica C Kissinger ; Nicolas Lackman ; Stacey A Lapp ; Mustafa Nural ; Nirav Patel ; Mariko S Peterson ; Gregory K TharpSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca mulatta ; Plasmodium knowlesiThis project is part of the Malaria Host-Pathogen Interaction Center (MaHPIC) - is a transdisciplinary malaria systems biology research program initially supported by an NIH/NIAID contract (# HHSN272201200031C, 2012-2017; see http://www.systemsbiology.emory.edu). The MaHPIC continues with ongoing support fro...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Macaca mulatta Plasmodium knowlesi Source Type: research

GSE111013 Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia [ATAC-seq]
Contributors : Andr é F Rendeiro ; Thomas Krausgruber ; Nikolaus Fortelny ; Fangwen Zhao ; Thomas Penz ; Matthias Farlik ; Linda C Schuster ; Amelie Kuchler ; Szabolcs Tasnády ; Marienn Réti ; Mátrai Zoltán ; Donat Alpar ; Csaba Bödör ; Christian Schmidl ; Christoph BockSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton Tyrosine Kinase (BTK) inhibitor ibrutinib induces a sustained anti-...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111014 Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia [scRNA-seq]
Contributors : Andr é F Rendeiro ; Thomas Krausgruber ; Nikolaus Fortelny ; Fangwen Zhao ; Thomas Penz ; Matthias Farlik ; Linda C Schuster ; Amelie Kuchler ; Szabolcs Tasnády ; Marienn Réti ; Mátrai Zoltán ; Donat Alpar ; Csaba Bödör ; Christian Schmidl ; Christoph BockSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton Tyrosine Kinase (BTK) inhibitor ibrutinib induces a sustained anti-CLL response i...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111015 Chromatin mapping and single-cell immune profiling defines the temporal dynamics of ibrutinib drug response in chronic lymphocytic leukemia
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensChronic lymphocytic leukemia (CLL) is a genetically, epigenetically, and clinically heterogeneous disease. Despite this heterogeneity, the Bruton Tyrosine Kinase (BTK) inhibitor ibrutinib induces a sustained anti-CLL response in patients from all risk groups, in stark contrast to widespread drug resistance in other heterogeneous cancers. To understand the dynamics of ibrutinib response against the backdrop of patient-specific and heterogeneous disease manifestations, we f...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111032 Heterochromatin drives organization of conventional and inverted nuclei
Contributors : Martin Falk ; Yana Feodorova ; Natasha Naumova ; Maxim Imakaev ; Bryan Lajoie ; Heinrich Leonhardt ; Boris Joffe ; Job Dekker ; Fudenberg Geoffrey ; Irina Solovei ; Mirny LeonidSeries Type : OtherOrganism : Mus musculusThe mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer s...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE111290 Gene expression profiling of the Arabidopsis Mediator MED5 mutants ref4-1 and ref4-3, CDK8 mutant cdk8-1 and ref4-3 cdk8-1
Contributors : Xiangying Mao ; Clint ChappleSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaPurpose: To identify changes in gene expression in ref4-3 mutant that contribute to the mutant ’s altered growth and metabolite accumulation by comparing differential gene expression in ref4-3 and ref4-3 cdk8-1.Methods: Gene expression profiles were generated from 20-day-old, pooled Arabidopsis rosettes in biological triplicate, by paried-end sequencing of 100 bp fragments using Illumina HiSeq 2500. The sequence reads that passed quality filters were aligned to the TAIR10 referenc...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE111823 Next Generation Sequencing Facilitates Quantitative Analysis of 0 and 5 Gy HuR binding RNAs
Conclusions: Our study represents the first detailed analysis of HuR binding RNAs between 0 and 5 Gy irradiation generated by RNA-seq technology. This study contributes to our understanding of the role of HuR inresponse to radiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE114881 Expression data from C. elegans exposed to pristine and aged ZnO manufactured nanoparticles
Contributors : Olga Tsyusko ; Daniel StarnesSeries Type : Expression profiling by arrayOrganism : Caenorhabditis elegansCaenorhabditis elegans were exposed at EC30 for 48 hr at L1 stage to ZnSO4, pristine ZnO-MNPs, phosphate aged pZnO-MNPs and sulfidized sZnO-MNPsWhole genome whole trascript microarrays were used to examine and compare global gene expression profiles among treatments (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Caenorhabditis elegans Source Type: research

GSE115610 Genome Wide Methylation Analysis of Organellar DNA in MR219 Indica Rice Cultivar
Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Oryza sativa Indica Group Source Type: research

GSE117340 Beadarray expression analysis to identify how LILRB2 blockade may affect transcriptional networks in M(LPS) and M(IL4)
Contributors : William Van Der Touw ; Shu-Hsia ChenSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe performed Illumina microarrays to identify how LILRB2 blockade may affect transcriptional networks in M(LPS) and M(IL4). To compare M(LPS) and M(IL4) populations helped define markers and pathway networks associated with M1 vs. M2-like functional phenotypes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE119126 YPR2 is a light dependent regulator of carbon and secondary metabolism in Trichoderma reesei
Contributors : Monika Schmoll ; Eva HitzenhammerSeries Type : Expression profiling by high throughput sequencingOrganism : Trichoderma reeseiWe show that YPR2, a transcription factor associated with the SOR cluster, has functions beyond regulation of this cluster in carbon and secondary metabolism and exerts its major function in darkness. It impacts production of secondary metabolites, particularly of Alamethicin and Orsellinic acid. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Trichoderma reesei Source Type: research

GSE120658 MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Contributors : Bruno Arca ; Alessio ColantoniSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Anopheles coluzziiDuring blood feeding haematophagous arthropods inject into their hosts a cocktail of salivary proteins whose main role is to counteract host haemostasis, inflammation and immunity. However, animal body fluids are known to also carry miRNAs. To get insights into saliva and salivary gland miRNA repertoires of the African malaria vector Anopheles coluzzii we used small RNA-Seq and identified 214 miRNAs, including tissue-enriched, sex-biased and putative novel anopheline miRNAs. Notewort...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Anopheles coluzzii Source Type: research

GSE121185 Transcriptional profile of the liver of zebrafish after feeding with 0% or 25% dietary maize substitution
Contributors : I J Gabri ëls ; L Vergauwen ; M De Boevre ; S Van Dongen ; R Blust ; S De Saeger ; M Eeckhout ; M De Loose ; D KnapenSeries Type : Expression profiling by arrayOrganism : Danio rerioFor the toxicological risk assessment of genetically modified (GM) food components, the European Food Safety Agency advises to use an adapted version of the 90-day oral toxicity study in rodents, originally designed for the toxicity testing of chemicals. Since in GM crop testing scenarios the crop under evaluation is specifically intended as a food / feed component, some testing aspects are conceptually different from testin...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Danio rerio Source Type: research

GSE121976 HOXC6 affects the malignant phenotype of esophageal squamous cell carcinoma cells
Contributors : Li Tang ; Yong Cao ; Xueqin Song ; Xiaoyan Wang ; Yan Li ; Minglan Yu ; Mingying Li ; Xu Liu ; Fang Huang ; Feng Chen ; Haisu WanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHOXC6 is a member of the HOX family, and its aberrant expression has been verified in a variety of cancers, such as prostate, breast,nasopharyngeal carcinoma,gastric, and ovarian cancers.Some studies suggest that HOXC6 might be involved in tumor initiation and progression.However, the role of HOXC6 in esophageal squamous cell carcinoma cells has not been fully investigated.Here we study how HOXC6...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122205 Transcriptomic profiles of retinal ganglion cells are defined by the magnitude of intraocular pressure elevation in adult mice
Contributors : Yong H Park ; Edwin J Ostrin ; Rui Chen ; Benjamin J FrankfortSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusElevated intraocular pressure (IOP) is the major risk factor for glaucoma, a sight threatening disease of retinal ganglion cells (RGCs) and their axons.   Despite the central importance of IOP, details of the impact of IOP elevation on RGC gene expression remain elusive.  We developed a novel 4-step immunopanning protocol to extract adult mouse RGCs with high fidelity and used it to isolate RGCs from wild type mice exposed to 2 weeks of IOP elevat ion ...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122968 transilice - Effects of silicon (Si) supply on leaf and root transcriptomes
Contributors : Jos é Caius ; Philippe Etienne ; Philippe Laine ; Ludivine Taconnat-Soubigou ; Véronique BrunaudSeries Type : Expression profiling by high throughput sequencingOrganism : Brassica napusngs2017_08_brasilice-transilice - What are the genes with modulated expression in response to brassica napus treatment (1.7mM, One week, root supply)-Brassica napus were grown on hydropnic conditions using Hoagland nutrient solution containing or not 1.7 mM of Si (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Brassica napus Source Type: research

GSE123071 Neural cell adhesion molecule 1 (NCAM1; CD56) promotes leukemogenesis and confers drug resistance in acute myeloid leukemia.
In this study we investigated the impact of aberrant NCAM1 expression on leukemogenesis, drug resistance and its role as a biomarker to guide therapy.Gene expression profiling was performed with RNA-seq in three cell lines (SKM-1, NOMO-1, MOLM-14) after doxycycline-mediated induction of scrambled shRNA or shNCAM1 at timepoint 72 hours. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE123326 Transcriptomic analysis of the Xrn1 depletion by Auxin-degron shutoff
Contributors : Jos é E Pérez-Ortín ; José García-MartínezSeries Type : Expression profiling by arrayOrganism : Saccharomyces cerevisiaeThe goal of the project was to study the effects on transcription and mRNA stability of the Xrn1 sudden depletion. We analyzed the effect of Xrn1 depletion caused by protein degradation of an Auxin-degron fusion on the transcription rates, mRNA stabilities and mRNA levels by doing Genomic Run-On (GRO) experiments at 30 min after Auxin addition with a control at 0 min. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Saccharomyces cerevisiae Source Type: research

GSE123602 Low-input chromatin profiling in Arabidopsis endosperm using CUT & RUN
Contributors : Mary Gehring ; Xiao-yu ZhengSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaEndosperm is an essential seed tissue with a unique epigenetic landscape. During endosperm development, differential epigenetic regulation of the maternal and paternal genomes plays important roles in regulating gene expression, especially at imprinted genes. Profiling the endosperm epigenetic landscape on a genome-wide scale is challenging due to its small size, mode of development, and close association with maternal tissue. Here, we applied a low input chromatin profilin...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE124302 LncRNA Spehd regulates hematopoietic stem cells and progenitors and is required for multilineage differentiation
Contributors : M J Delas ; Benjamin T Jackson ; Gregory J HannonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusLong non-coding RNAs (lncRNAs) show patterns of tissue- and cell-type-specific expression that are very similar to those of protein coding genes and consequently have the potential to control stem and progenitor cell fate decisions along a differentiation trajectory. To understand the roles that lncRNAs might play in hematopoiesis, we selected a subset of mouse lncRNAs with potentially relevant expression patterns and refined our candidate list using evidence of conserved ex...
Source: GEO: Gene Expression Omnibus - February 22, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research