GSE109904 450K analysis of pediatric histiocytic sarcomas and anteceding hematologic malignancies
Contributors : Pascal Johann ; Matthias BleekeSeries Type : Methylation profiling by arrayOrganism : Homo sapiensThe dataset contains 450K array data on 3 cases of histiocytc sarcomas and corresponding leukemias (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE116562 Expression data from human ovarian cancer cell line
Contributors : Ning Sheng ; Shaohua FanSeries Type : Expression profiling by arrayOrganism : Homo sapiensLASS2 was used to identified as a novel suppressor in cancer development and progression. We explored roles of LASS2 in ovarian cancer invasion and metastasis. Lenti-LASS2 and Lenti-vector cells were constructed in 3AO cells through a lentiviral vector system.We preformed global gene expression analysis between Lenti-LASS2 and Lenti-vector cells in accordance with standard Aglient protocols to explore differentially expressed genes and signaling pathways involved by LASS2 overexpression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116563 LRH-1 Mitigates Intestinal Inflammatory Disease by Maintaining Epithelial Homeostasis and Cell Survival
We report the gene expression changes in murine small intestinal organoids following deletion of LRH-1 (NR5A2) and humanization by expression of human LRH-1 in mouse LRH-1 knockout organoids. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116564 Programmed Cell Death Ligand 1 (PD-L1) Signaling Regulates Macrophage Proliferation and Activation
Contributors : Genevieve Hartley ; Lyndah ChowSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used in vitro and in vivo models to investigate PD-L1 signaling in macrophages and the effects of PD-L1 antibody treatment on Tumor associated macrophage responses (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116572 RNA-seq analysis of transcriptomes of Noc4L deficient and the Nco4L sufficient Treg cells
Contributors : Xueping Zhu ; Xuyu ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo gain in depth transcriptional information about the Noc4L deficeint an Noc4L sufficient Tregs, we performed RNA-seq analysis to compare the transcriptomes of Noc4L sufficient (CD4+GFP+CD62Lhigh, Het) and Noc4L deficient (CD4+GFP+CD62Lhigh, Het) Tregs activated in vitro with Dynabeads for 48 hours or 72 hours. We found ~25 unique genes with differential expression between the Noc4L deficient and Noc4L sufficient Treg cells when activated for 48 hours in vitro. And ~100 unique genes with differentia...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116575 Overexpression of miR-155 alters the hierarchy of gene master regulators in the adenocarcinomic human alveolar basal epithelial cell line A549
Contributors : Dumitru A Iacobas ; Sanda Iacobas ; Katrien Van Roosbroeck ; George A CalinSeries Type : Expression profiling by arrayOrganism : Homo sapiensSeveral reports indicated that miR155 is upregulated in many cancer forms, including lung adenocarcinoma. Studies perfomed in Calin's lab (e.g. Van Roosbroeck et al., Clin Cancer Res, doi: 10.1158/1078-0432.CCR-16-1025) demonstrated that miR-155 induces resistance to multiple chemotherapeutic agents. We hypothesize that the induced resistance is related to the rearrangement of cellular gene hierarchy. In previous papers (Iacobas& Iacobas, Cancer& Oncol Res DOI:1...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116579 Newly identified Aspergillus nidulans PKA targets play a role in carbon-catabolite repression
Contributors : Liliane F Ribeiro ; Jyothi Kumar ; Steven Harris ; Mark R MartenSeries Type : Expression profiling by high throughput sequencingOrganism : Aspergillus nidulansA transcriptomic assessment of a kinase deletion mutant ( ΔpkaA) and a control strain revealed many cellular activities this kinase is impacting. Studies were conducted in the model filamentous fungi, Aspergillus nidulans¸ under rich growth conditions. PkaA is a known kinase that mediates a wide range of processes including: nutrient sensing, stress resp onses, regulation of metabolism, as well as development and pathogenicity. Here, fungi ...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Aspergillus nidulans Source Type: research

GSE116581 fruitENCODE: An encyclopedia of DNA elements for fruit ripening
Contributor : Silin ZhongSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thaliana ; Carica papaya ; Citrullus lanatus ; Cucumis melo ; Cucumis sativus ; Fragaria vesca ; Malus domestica ; Musa acuminata AAA Group ; Oryza sativa ; Prunus persica ; Pyrus x bretschneideri ; Solanum lycopersicum ; Vitis viniferaFleshy fruits evolved independently multiple times during angiosperm history, including the use of ethylene for the initiation and maintenance of ripening. ENCOD...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Carica papaya Citrullus lanatus Cucumis melo Cucumis Source Type: research

GSE116582 Transcriptome analysis of top3A-2 complementation lines in Arabidopsis thaliana
Contributors : Annika Dorn ; Holger Puchta ; Alexander KnollSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaTranscriptome analysis of Attop3A-2 mutant lines in comparison to wild type plants and Attop3A-2::TOP3 α-N-Term complementation lines in comparison to wild type plants (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE116583 Alveolar Macrophages after Murine Lung Transplant
The objective of this study was to examine transcriptional changes in alveolar macrophages early after reperfusion in a model of murine lung transplant. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116584 Expression data from young adult, and post-mortem mouse satellite cells
Contributors : Francesca Pala ; S ébastien MellaSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptomic analysis of FACS-sorted Pax7nGFP quiescent skeletal muscle satellite cells cells from old, and post-mortem mice. Results provide knowledge about the molecular mechanisms underlying age-related skeletal muscle satellite cells homeostasis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116585 Expression data from young adult, and aged mouse satellite cells
Contributors : Siham Yennek ; S ébastien MellaSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptomic analysis of FACS-sorted Pax7nGFP quiescent skeletal muscle satellite cells cells from young, and old mice. Results provide knowledge about the molecular mechanisms underlying age-related skeletal muscle satellite cells homeostasis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116586 Expression data from young adult, aged, and post-mortem mouse satellite cells
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116587 Swarmer Cell Development of the Bacterium Proteus mirabilis Requires the Conserved Enterobacterial Common Antigen Biosynthesis Gene rffG
Contributors : Murray Tipping ; Karine GibbsSeries Type : Expression profiling by high throughput sequencingOrganism : Proteus mirabilisIndividual cells of the bacterium Proteus mirabilis can elongate up to 40- fold on surfaces before engaging in a cooperative surface-based motility termed swarming. How cells regulate this dramatic morphological remodeling remains an open question. In this paper, we move forward the understanding of this regulation by demonstrating that P. mirabilis requires the gene rffG for swarmer cell elongation and subsequent swarm motility. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Proteus mirabilis Source Type: research

GSE116589 Identification and validation of circHIPK3 is upregulated in colorectal cancer and characterization of its role in promoting carcinogenesis
Contributors : Fanghua Qiu ; Jiewen GuoSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensIn order to confirm that circHIPK3 in colorectal cancerand characterization of its role in carcinogenesis, verified the expression level of circHIPK3 in additon 18 samples, and further collected 30 health controls and 30 colorectal cancer patients for exosome detection. The present study identified circHIPK3 is higher expression in CRC tissues and exosome of CRC patients. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116594 Comparison of gene expression pattern between wild-type and RhoE knockout embryo hearts
Contributors : Xiangsheng Yang ; Lixia Diao ; Jing Wang ; Yuan Dai ; Jiang ChangSeries Type : Expression profiling by arrayOrganism : Mus musculusRhoE is a small GTPase that regulates actin cytoskeleton organization and cell migration. This analysis aimed at exploring the physiological function of RhoE in heart by means of knockout mouse model.We used microarrays to compare differentital gene expression profiles in wild-type and RhoE knockout embryo hearts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116605 Combined RNA-seq and RAT-seq mapping of long noncoding RNAs in pluripotent reprogramming
Contributors : Jifan Hu ; Zhonghua DuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA transcriptome sequencing (RNA-Seq) and RNA reverse transcription-associated trap sequencing (RAT-Seq) were usded to map long noncoding RNA (lncRNAs) in reprogramming of fibroblasts into pluripotency (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116613 TBK1 suppresses RIPK1-driven apoptosis and inflammation during development and in aging
Contributors : Daichao Xu ; Junying YuanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAging is a major risk factor for both genetic and sporadic neurodegenerative disorders. However, it is unclear how aging interacts with genetic predispositions to promote neurodegeneration. Here we investigate how partial loss-of-function of TBK1, a major genetic cause for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) comorbidity, leads to age-dependent neurodegeneration. We show that TBK1 is an endogenous inhibitor of RIPK1 and the embryonic lethality of Tbk1-/- mice is dep...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116615 Comparative Transcriptomics of Limb Regeneration: Identification of Conserved Expression Changes Among Three Species of Ambystoma
Contributors : Varun B Dwaraka ; Jeramiah J Smith ; M R Woodcock ; S R VossSeries Type : Expression profiling by arrayOrganism : Ambystoma mexicanumTranscriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model – Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. ma culatum. Salamanders were administered forelimb amputa...
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Ambystoma mexicanum Source Type: research

GSE116616 Expression data of whole genome from new diagnostic AML patients (with or without EMI) and healthy volunteers
Contributors : Yinghua Li ; Zhibo GuoSeries Type : Expression profiling by arrayOrganism : Homo sapiensWhole Genome microarray was conducted to further explore the underlying gene expression alterations in extramedullary infiltration (EMI) of AML. 4 matched samples from EMI, non-EMI AML patients and healthy volunteers were selected. Mononuclear cells from 12 bone marrow samples were separated according to protocols. RNA was then extracted and hybridization for further microarray analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116617 Expression data of circRNA from new diagnostic AML patients (with or without EMI) and healthy volunteers
Contributors : Yinghua Li ; Zhibo GuoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensCircRNA microarray was conducted to further explore the underlying circRNA expression alterations in extramedullary infiltration (EMI) of AML. 4 matched samples from EMI, non-EMI AML patients and healthy volunteers were selected. Mononuclear cells from 12 bone marrow samples were separated according to protocols. RNA was then extracted and hybridization for further microarray analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 4, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE116500 Spec-seq unveils transcriptional subpopulations of antibody-secreting cells following influenza vaccination
Contributors : Karlynn E Neu ; Min Huang ; Jennifer La ; Marcos C Vieira ; Kangchon Kim ; Nai-Ying Zheng ; Mario Cortese ; Karla T Rojas ; Carole Henry ; Dustin Shaw ; Charles L Dulberger ; Bali Pulendran ; Sarah Cobey ; Aly A Khan ; Patrick C WilsonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensVaccines are among the most effective public health tools for combating certain infectious diseases such as influenza. The role of the humoral immune system in vaccine-induced protection is widely appreciated; however, our understanding of how antibody specificities relate to B cell function ...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE70549 RNA-Seq matched to ribosome profiling over a zebrafish developmental timecourse
Contributors : Guo-Liang Chew ; Andrea Pauli ; Alexander F SchierSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioRNA-Seq data that is sample matched to a previous ribosome profiling dataset GSE46512 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE81943 Hepatic transcriptome of wildtype and Cugbp1 knockout mouse neonates.
Contributors : Nikolai Timchenko ; Rebekah KarnsSeries Type : Expression profiling by arrayOrganism : Mus musculusWe characterize the hepatic transcriptome of wildtype and Cugpb1 knockout mice at day 3 of life using the Agilent Whole Mouse Genome Oligo Microarray, focusing on the role of Cugbp1 in the differentiation of hepatic stem cells into hepatocytes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE85189 ATRA mediated regulation of chromatin state
Contributor : C ChangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensGenome-wide ChIP is performed to examine ATRA-mediated regulation of Tet2 chromatin complex associtaion on different promoter regions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100388 Dietary intake of antioxidant curcumin reduces eIF2 phosphorylation and diacylglycerol and glycerolipid contents in white adipose tissue of obese mice
Contributor : M KoboriSeries Type : Expression profiling by arrayOrganism : Mus musculusTo elucidate the bioactive property of the dietary antioxidant curcumin, we examined tissue distribution and the gene expression- and lipidomic-profiles in epididymal white adipose tissue (eWAT) of the diet-induced obese mice. Dietary intake of curcumin (0.1% W/W) didn ’t affect the eWAT weight and the plasma lipid levels but reduced the levels of lipid peroxidation marker in eWAT. Curcumin was a slightly accumulated in eWAT and altered the gene expression associated with eukaryotic translation initiation factor 2 (EIF2) signaling...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE101982 Expression data from LNCaP clonal isolates over-expressing HIST1H1A or Vector Control.
Contributors : Kendra A Williams ; Minnkyong Lee ; Jean M Winter ; Derek Gildea ; Carla Calagua ; Natasha Curry ; Jens Lichtenberg ; Huihui Ye ; Nigel P CrawfordSeries Type : Expression profiling by arrayOrganism : Homo sapiensHIST1H1A is a member of the linker histone family that is involved in correct folding and compaction of chromatin.We used lentival transduction to stably express HIST1H1A in human prostate cancer LNCaP cells and examined the changes in gene expression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE102129 LiCl treated KG1a cells, irradiated at 4Gy and 8Gy, incubated for 48hr
Contributors : Yogesh K Verma ; Gangenahalli U GuruduttaSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression following ionizing radiation exposure to LiCl treated cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104366 Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species
Conclusions: Our integrative analysis clearly reveals the important and conserved role of the methylation level of the first intron and its inverse association with gene expression regardless of tissue and species. These findings not only contribute to our basic understanding of the epigenetic regulation of gene expression but also identify the first intron as an informative gene feature regarding the relationship between DNA methylation and gene expression where future studies should be focused. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Dicentrarchus labrax Source Type: research

GSE104622 Establishment of adult epidermal organoid cultures from canine hair follicles and interfollicular epidermis
Contributors : Dominique J Wiener ; Onur Basak ; Priyanca Asra ; Kim Boonekamp ; Kai Kretzschmar ; Angelos Papaspyropoulos ; Hans CleversSeries Type : Expression profiling by high throughput sequencingOrganism : Canis lupus familiarisThe epidermis and associated appendages ensure a number of critical functions necessary for survival and social interactions. Perturbations of epidermal stem cell homeostasis lead to a variety of skin diseases affecting humans and dogs. Therefore, the establishment of an in vitro system to investigate canine epidermal stem cells, representing a model for human diseases, is essential. Here we r...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Canis lupus familiaris Source Type: research

GSE108669 LPS and Telmisartan co-treatment of microglial BV2 cells
Contributors : Abdel Elkahloun ; Juan SaavedraSeries Type : Expression profiling by arrayOrganism : Mus musculusLPS and Telmisartan co-treatment of microglial BV2 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE108670 LPS, Telmisartan and GW9662 co-treatment of microglial BV2 cells
Contributors : Abdel Elkahloun ; Juan SaavedraSeries Type : Expression profiling by arrayOrganism : Mus musculusLPS, Telmisartan and GW9662 co-treatment of microglial BV2 cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE108671 LPS, Telmisartan and GW9662 treatment of microglial BV2 cells
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE109376 Cardiac fibroblasts behave differently to isoproterenol-induced injury based on their genetic variability
This study compare the fibrotic response of ISO-treated hearts in 3 strains of mice (B6, C3H and KK) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111248 A Virus-acquired Host Cytokine Controls Systemic Aging by Antagonizing Apoptosis
Contributors : Mohamed Mlih ; Jason KarpacSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterAging is characterized by degeneration of unique tissues. However, dissecting the interconnectedness of tissue aging remains a challenge. Here, we employ a muscle-specific DNA damage model in Drosophila to reveal secreted factors that influence systemic aging in distal tissues. Utilizing this model, we uncovered a cytokine, Diedel, that when secreted from muscle or adipose can attenuate age-related intestinal tissue degeneration by promoting proliferative homeostasis of stem cells. Die...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE113326 Epigenetic reprogramming in hepatic carcinogenesis
Contributors : Ying-Ying Lee ; Myth T Mok ; Feng Wu ; Alfred S ChengSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusGenomic sequencing of hepatocellular carcinoma (HCC) uncovers a paucity of actionable mutations, underscoring the necessity to exploit epigenetic vulnerabilities for therapeutics. In HCC, EZH2-mediated H3K27me3 represents a major oncogenic chromatin modification, but how it modulates the therapeutic vulnerability of signaling pathways remains unknown. Here, we identified that EZH2 maintains H3K27 methylome through epigenetic silencing of specific gene sets....
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE114410 DNA topoisomerase and supercoil accumulation across yeast genome
Contributors : Yathish J Achar ; Mohamood Adhil ; Marco FoianiSeries Type : Genome binding/occupancy profiling by genome tiling arrayOrganism : Saccharomyces cerevisiaeDNA toposiomserases assist DNA replication& transcription events by controlling supercoiling alterations. We investigated supercoil distribution across yeast genome and compared with accumulation of RNA pol2 and DNA topoisomerases particularly in S-phase. Our data indicate that Top2 along with Hmo1 maintain negative supercoil at gene boundaries by stabilizing alternative DNA structures.To understand how DNA super helical tension accumulate across the gen...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by genome tiling array Saccharomyces cerevisiae Source Type: research

GSE114444 Effect of chromatin architectural proteins; Top2 and Hmo1 on transcription levels in yeast
Contributors : Yathish J Achar ; Mohamood Adhil ; Marco FoianiSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeDNA topoisomerase-2 and high mobility group protein Hmo1 are known to regulate chromatin architecture by regulating gene boudaries. Here we report how these proeins effect global RNA level after inactivating. Our data indicate that inactivating Hmo1 has drastic effect on transcription levels of 20% yeast genes, however this phenomenon can slighty rescued by inactivating Top2 functions. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE114474 Expression profiling of clonally derived skeletal progenitors from mouse bone marrow
Contributors : Konstantinos Anastassiadis ; Maria RostovskayaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBone marrow stromal cells (BMSCs) were isolated from the femora and tibiae of irtTA-GBD*-TAg transgenic mice. Using cellular cloning we established skeletal progenitors with distinct differentiation properties and analysed their transcriptome. Unipotent osteogenic and adipogenic cells expressed specific transcriptional programs whereas bipotent clones combined expression of those genes and did not show a unique signature. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114475 Expression profiling of mouse bone marrow skeletal progenitors with osteogenic and adipogenic potential and adipogenic progenitors treated with IFN γ.
Contributors : Konstantinos Anastassiadis ; Maria RostovskayaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBone marrow stromal cells (BMSCs) were isolated from the femora and tibiae of irtTA-GBD*-TAg transgenic mice. Using cellular cloning we established skeletal progenitors with unipotent osteogenic and adipogenic properties. Previous RNA-seq analysis of more progenitor types revealed differential expression in members of the Interferon-gamma (IFN γ) signaling pathway. Treatment of adipogenic progenitors with IFNγ inhibited adipogenesis and promoted osteogenesis. RNA-se...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114891 Human peripheral blood mononuclear cells (PBMC): post- ECP treatment vs. pre-treatment (baseline)
Contributor : Xiao NiSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional profiling of human peripheral mononuclear cells in patients with leukemic cutaneous T-cell lymphoma (CTCL): a pilot study of effects of extracorporeal photopheresis (ECP) in clinically responsive and non-responsive/resistant patients (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE115025 Transcriptional profile of monocytes in the colon in response to C. rodentium infection
Contributors : Ken Cadwell ; Patricia Marton ; Eugene RudenskySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTranscriptional profile of monocytes in the colon in response to C. rodentium infection (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116466 The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (iCLIP)
Contributor : Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNumerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3 ’UTR usage analysis using poly...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116468 The effect of cellular context on miR-155 mediated gene regulation in four major immune cell types (PolyA-Seq)
Contributor : Alexander Y RudenskySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNumerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3 ’UTR usage analysis using poly...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116472 Single-molecule nascent RNA sequencing reveals regulatory domain architecture ant promoters and enhancers
Contributors : Jacob M Tome ; Nathaniel D Tippens ; John T LisSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusCoPRO adapts PRO-cap for paired end sequencing, and includes a total of three different libraries that were enriched for either capped nascent RNAs only, uncapped nascent RNAs only, or both. With paired end sequencing, each read tells us where an RNA polymerase molecule initiated, and then where its active site is located. Comparison of the libraries for different capping states allows us identify the precise location of pausing, and of where nascent RNA...
Source: GEO: Gene Expression Omnibus - July 2, 2018 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE116369 Discovering human diabetes-risk gene function with genetics and physiological assays
Contributors : Heshan Peiris ; Seung KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo delineate the effects of BCL11A (a type 2 diabetes risk gene) in human beta cell function we knockdown BCL11A in primary human beta cells and generated and sequenced RNA-seq libraries from 4 human donors (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE56113 Superiority of spatially fractionated over broad beam synchrotron radiotherapy
Contributors : Audrey Bouchet ; Elke Br äuer-Krisch ; Yolanda Prezado ; Michèle El Atifi ; Léonid Rogalev ; Céline Le Clec’h ; Jean Laissue ; Laurent Pelletier ; Géraldine Le DucSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusTranscriptomic response of tumoral and normal brain tissue, treated with the MRT irradiation or the BB irradiation, after 6 h, 48 h, 8 days, 15 days, using Affymetrix GeneChip ® Rat 230_ 2. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE58646 Comparison of the transcriptomic profiles of two human glioma cell lines, U87 and Glio6.
Contributors : Ulysse Gimenez ; Adriana-T Perles-Barbacaru ; Michele El Atifi ; Florence Appaix ; Didier Wion ; Fran çois Berger ; Boudewijn Van der Sanden ; Hana LahrechSeries Type : Expression profiling by arrayOrganism : Homo sapiensUsing Affymetrix GeneChip ® Human Genome U133 Plus 2.0 Array, we compared the gene expression profiles between the glioma cell lines U87 and Glio6, cultured at 3% of oxygene. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE62688 Transcriptome profiling based study of early gene responses in susceptible and tolerant rat lung tissues during acute hypobaric hypoxia
Conclusion: The differential gene expression patterns in different experimental sets elucidated the physiological mechanisms associated with progressive damage in the lung tissues of susceptible and normal (moderate) rats, and tissue protective measures in tolerant rats during acute hypobaric hypoxia. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE70127 The epigenetic and transcriptional basis of a developmental transition from brown to white adipose tissue
Contributors : Aaron Statham ; Ross TellamSeries Type : Methylation profiling by high throughput sequencingOrganism : Ovis ariesBrown and white adipose tissues are functionally and morphologically distinct. Theformer tissue has a primary role in maintaining thermogenesis in new born mammals while the latter acts as an energy storage vehicle that enhances survival when food is limiting. Both tissues are involved in maintaining energy homeostasis in adults and are strongly implicated in chronic metabolic diseases associated with obesity in humans. The perirenal adipose depot in sheep undergoes a relatively rapid transition f...
Source: GEO: Gene Expression Omnibus - July 1, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Ovis aries Source Type: research