GSE99559 SQSTM1/p62-directed metabolic reprogramming is required to prevent neurodegenerative disease
Contributors : Javier Calvo-Garrido ; Camilla Maffezzini ; Florian A Schober ; Paula Clemente ; Elias Uhlin ; Malin Kele ; Henrik Stranneheim ; Nicole Lesko ; Helene Bruhn ; Per Svenningsson ; Anna Falk ; Anna Wedell ; Christoph Freyer ; Anna WredenbergSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNeurodegenerative disorders are an increasingly common and irreversible burden on society, often affecting the ageing population, but their aetiology and disease mechanisms are poorly understood. Studying monogenic neurodegenerative diseases, with known genetic cause, provides an opportuni...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100521 Transcriptional and Functional Diversity of Macrophage Repolarization: Implications in Chronic Inflammation and Cystic Fibrosis
We examined the transcriptional and functional significance of macrophage repolarization from an “M1” (LPS-stimulated) towards an “M2” phenotype using 5 stimuli. We found that macrophages exhibit highly diverse responses to distinct M2-polarizing stimuli. Specifically, we observed that IL-10 abrogated LPS-tolerance allowing for rapid restoration of LPS responsiveness. In contrast, IL-4 enhanced LPS-tolerance, dampening pro-inflammatory responses after repeat LPS challenge. We found enrichment of phagocytosis-associated pathways in macrophages stimulated with IL-10, leading them to display the greate...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE103070 Transcriptome profile of wildtype and Ret homozygote null mouse guts at E10.5 ,E12.5 and E14.5
Contributors : Sumantra Chatterjee ; Aravinda ChakravartiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTotal mRNA seq was perfomed on widtype and Ret null mouse embryonic gut at 3 stages of devlopment- E10.5, E12.5 and E14.5 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE103541 DNA methylation profiles of Purified Blood Cell types
Contributors : Jonathan Mill ; Eilis Hannon ; Joe BurrageSeries Type : Methylation profiling by arrayOrganism : Homo sapiensDNA methylation profiles for CD4 T cells, CD8 T cells, B cells, Monocytes and Granulocytes purified from 28 individuals (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE103852 RNAseq to understand the host transcriptome during nontuberculous mycobacterial lung infection
Contributors : Jennifer R Honda ; Thomas Danhorn ; Kendra N Walton ; Brian P O'Connor ; Sonia M LeachSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe sought to elucidate the differentially expressed host factors in bronchoalveolar lavage cells (BALc) from nontuberculous mycobacteria (NTM)-infected subjects by studying the host transcriptome in during infection. A heatmap was created from the normalized expression of selected genes that showed statistically significant differential expression between NTM-infected and uninfected subjects. Genes with similar expression patterns were gr...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE103946 Antagonistic action of PHYA and PHYB is involved in FR-dependent leaf senescence in Arabidopsis accessions
In conclusion, we propose that PHYs-regulated genes, including WRKY6, are involved in latitudinal leaf senescence in FR and this regulatory mode may contribute to latitudinal adapta-tion by responding FR, as a piece of geographical information. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE108223 DNA and Histone Methyltransferase Inhibitors Cooperate to Increase Viral Mimicry in Ovarian Cancer Cells
Contributors : Minmin Liu ; Peter A JonesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTotal RNA sequenceing method was used to compare the differential expression of genes in A2780, CAOV3, PEO14, and OAW42 cells with G9Ai, 5-aza-CdR and combination treatment compared to untreated cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108241 Exploring transcriptomic landscapes in red cell populations, in their extracellular vesicles and on single cell level
Contributors : Erja Kerkel ä ; Jenni Lahtela ; Antti Larjo ; Laura Mäenpää ; Pirkko MattilaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCirculating human red blood cells (RBCs) consist of mature erythrocytes, and immature reticulocytes. As being anucleated cells, RBCs lack typical, abundant transcriptomes but are known to contain low amounts of diverse long transcripts and microRNAs. The exact role and importance of these RNAs is, however, lacking. To study this further, we have explored the RNA content of RBCs as well as extracellular vesicles of RBCs using nex...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109974 RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis
Contributors : Jiafu Zhu ; Min Liu ; Xiaobin Liu ; Zhicheng DongSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Arabidopsis thalianaRNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted mammalian Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carbox...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Arabidopsis thaliana Source Type: research

GSE110126 The impact of DSF and C23 on P. aeruginosa physiology
Contributor : Shi-qi AnSeries Type : Expression profiling by arrayOrganism : Pseudomonas aeruginosaTo verify the imapct of DSF and C23 on P. aeruginosa during infectionWe used microarray to compare the effects of adding either DSF alone or DSF with C23 on P. aeruginosa gene expression during mouse lung infection relative to the gene expression of P. aeruginosa in the mouse lung with no compound. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Pseudomonas aeruginosa Source Type: research

GSE111885 Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HaCaT cells)
Contributors : Yuki Sawai ; Katsuhiro UzawaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo obtain differentially expressed genes associated with cetuximab induced cytotoxicity we analyzed RNA samples using whole genome microarray expression profiling as a discovery platform to identify genes . Two kinds of RNA samples were extracted from HaCaT and HEK 293 cell; without cetuximab and incubation for 24 hours with 1.63 μM (fixed maintenance dose) cetuximab. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111886 Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells (HEK 293 cells)
Contributors : Yuki Sawai ; Katsuhiro UzawaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo obtain differentially expressed genes associated with cetuximab induced cytotoxicity we analyzed RNA samples using whole genome microarray expression profiling as a discovery platform to identify genes . Two kinds of RNA samples were extracted from HaCaT and HEK 293 cell; without cetuximab and incubation for 24 hours with 1.63 μM (fixed maintenance dose) cetuximab. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111887 Molecular mechanisms and potential therapeutic drugs linking to cetuximab-induced reactions in human cells
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 - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112236 Cell type-specific endometrial transcriptome changes in comparison of equine endometrium samples collected on Day 12 of pregnancy and Day 12 of the estrous cycle
Contributors : Iside Scaravaggi ; Stefan BauersachsSeries Type : Expression profiling by high throughput sequencingOrganism : Equus caballusThe results of endometrial gene expression studies during the time of conceptus migration (Days 8 to 16) did not provide final conclusions on possible mechanisms of maternal recognition of pregnancy (MRP) in the mare. This finding called for the analysis of cell type-specific gene expression in the endometrium in response to the equine embryo, which could be the key for improved understanding of gene expression regulation in context of MRP. In a pilot study, we used laser capture micro...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Equus caballus Source Type: research

GSE112237 Endometrial transcriptome changes in comparison of equine endometrium samples collected on Day 12 of pregnancy and Day 12 of the estrous cycle
Contributors : Maximiliane Merkl ; Stefan BauersachsSeries Type : Expression profiling by high throughput sequencingOrganism : Equus caballusEstablishment and maintenance of pregnancy in equids is only partially understood. To provide new insights into early events of this process, we performed a systematic analysis of transcriptome changes in the endometrium at days 8 and 12 of pregnancy. Endometrial biopsy samples from pregnant and non-pregnant (Day 12) stages were taken from the same mares. Composition of the collected biopsy samples was analyzed using quantitative stereological techniques to determine proportions of su...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Equus caballus Source Type: research

GSE112275 Microarray analysis of Elavl2 knockout ovaries
Contributors : Yuzuru Kato ; Yumiko SagaSeries Type : Expression profiling by arrayOrganism : Mus musculusElavl2 knocout female mice show oocyte loss-phenotype shortly after birth. To reveal the involvement of Elavl2 in oogenic gene expression, embryonic and newborn ovaries were subjected to microarray analysis (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE113235 VEGFC Upregulates Trans-Lymphatic Colorectal Cancer Metastasis in the Liver via Recruiting Bone Marrow Derived Cells
In conclusion, VEGFC in CRC cells promoted trans-lymphatic metastasis of CRCLM by upregulation of lymphangiogenesis directly and indirectly via induction of macrophages derived from bone marrow cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE113304 Primordial follicle formation involves dynamic conversion of RNA regulatory proteins (RIP-seq data set)
Contributors : Yuzuru Kato ; Yumiko SagaSeries Type : OtherOrganism : Mus musculusLong-term reproductive ability in mammalian females is sustained by the successive consumption of the finite pool of primordial follicles, the most primitive ovarian follicles that arise from cystic-oocytes during oogenesis. However, mechanisms underlying the formation of primordial follicles are largely unknown. Here we show that dynamic conversion of RNA-regulatory proteins precedes the formation of primordial follicles in mice. We find that, whereas stress granules dominate in cystic-oocytes, those are replaced by processing-bodies prior t...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE113305 Primordial follicle formation involves dynamic conversion of RNA regulatory proteins
Series Type : Other ; Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Other Expression profiling by array Mus musculus Source Type: research

GSE113943 The response of the hypothalamus to leptin and a high-fat diet in mice
Contributors : Lynda M Williams ; Claus-Dieter Mayer ; Michael Muller ; Baukje de Roos ; Eva-Maria BachmairSeries Type : Expression profiling by arrayOrganism : Mus musculusEnergy homeostasis is regulated by the hypothalamus but fails when animals are fed a high-fat diet (HFD), and leptin insensitivity and obesity develops. We have used a microarray-based transcriptomics approach to identify novel genes regulated by HFD and leptin in the hypothalamus using mouse global arrays. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE114237 Matrix mineralization controls gene expression in osteoblasts
Contributors : Oxana Schmidt ; Johannes Wischmann ; R üdiger von Eisenhart-Rothe ; Philipp Mayer-Kuckuk ; Günther H Richter ; Günther RichterSeries Type : Expression profiling by arrayOrganism : Homo sapiensOsteoblasts are adherent cells. Under physiological conditions they attach to mineralized and non-mineralized osseous surfaces. However, how exactly osteoblasts respond to these different osseous surfaces is largely unknown. Our hypothesis was that the state of matrix mineralization provides a functional signal to osteoblasts. To assess the osteoblast response to mineralized compared to demineralized osse...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114373 Isolation of Heart Field Specific Cardiomyocytes from Differentiating Human Embryonic Stem Cells for Cardiac Regeneration
Contributors : James L Engel ; Arash Pezhouman ; Suhail Khoja ; Ngoc B Nguyen ; Rhys J Skelton ; W B Gilmore ; Debashis Sahoo ; David A Elliott ; Peng Zhao ; Reza ArdehaliSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAnalysis of TBX5 and non-TBX5 derived cardiomyocyte populations from differentiating hESCs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116516 Effect of ALOXE3 overexpression on primary murine hepatocyte gene expression profiles
Contributor : Brian DeBoschSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe demonstrate the effects of ALOXE3 overexpression on primary murine hepatocyte gene expression by high-throughput RNA sequencing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117014 RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis
Contributors : Jiafu Zhu ; Min Liu ; Xiaobin Liu ; Zhicheng DongSeries Type : OtherOrganism : Arabidopsis thalianaRNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted plant Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream th...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Other Arabidopsis thaliana Source Type: research

GSE117385 Host-pathogen transcriptomics of Mucor circinelloides spores phagocytosed by mouse macrophages
Contributors : Carlos Perez-Arques ; Maria-Isabel Navarro-Mendoza ; Victoriano Garre ; Francisco-Esteban NicolasSeries Type : Expression profiling by high throughput sequencingOrganism : Mucor circinelloides f. lusitanicus ; Mus musculusHere, we have studied the first stage of this infection —the interaction of Mucor circinelloides spores with phagocytic cells—from an integrated transcriptomic and functional perspective. Our transcriptomic results showed that a relevant gene network is remodelled in response to phagocytosis, enriched in crucial functions to survive the phagosome, su ch as nutritional adaptation...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mucor circinelloides f. lusitanicus Mus musculus Source Type: research

GSE117939 High throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites
Contributors : Mia K Mihailovic ; Jorge Vazquez-Anderson ; Yan Li ; Victoria Fry ; Praveen Vamalathas ; Daniel Herrera ; Richard A Lease ; Lydia M Contreras ; Warren B Powell ; Lydia M ContrerasSeries Type : OtherOrganism : Escherichia coliThese data were obtained using a recently-developed high throughput method to probe regional RNA accessibility by mimicking in vivo antisense hybridization. The method (INTERFACE) is an engineered RNA system (for use in E. coli) that exploits conserved bacterial mechanisms of translational stalling and Rho-dependent transcription termination mechanisms to quantify RNA hybridization (via ...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Other Escherichia coli Source Type: research

GSE117974 RNA sequencing of mouse liver cancer cell lines with YAP/TAZ mutations
Contributors : Matthew Chang ; Anwesha DeySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA from cell lines derived from YAP-S127A, YAP-5SA and TAZ-S89A mouse liver tumors. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0014900 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE118116 Comparison of the expression profiles of wild-type  Rhodobacter capsulatus and a GTA hyperproducer (DE442) by RNAseq.
Contributor : Paul FoggSeries Type : Expression profiling by high throughput sequencingOrganism : Rhodobacter capsulatus DE442 ; Rhodobacter capsulatus SB 1003Gene Transfer Agents (GTAs) are small virus-like particles that transfer random fragments of host bacterial DNA between cells. Unlike true viruses, whose primary aim is self-preservation, GTAs have no preference for the spread of their own genes. GTAs are typically produced from less than 1% of the population, making in-depth analysis of producer cells problematic. Here, we compared the transcriptome of wild-type  R. capsulatus and a GTA hyperproducer, DE44...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rhodobacter capsulatus DE442 Rhodobacter capsulatus SB 1003 Source Type: research

GSE118282 The gene expression profiles of human multiple myeloma cell lines transfected with miR-10a mimic
In this study, we investigated the biological property of the EVs and EV-miRNAs derived from BMSCs, aiming to establish the emerging strategies to target MM microenvironment to prevent tumor growth and spread.We found that the MM-BMSC-EVs enhanced the cell proliferation of RPMI8226. The EV-miRNA expression was different between MM-BMSCs and Normal-BMSCs, and some miRNAs, including miR-10a, were significantly up-regulated in the MM-BMSC-EVs. We then visualized with an in vitro model the uptake of Cy3-labeled miR-10a into RPMI8226 via EVs. To identify the function of miR-10a in MM cells, miR-10a mimic was transfected into RP...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE118516 Transcriptome analysis of control and TFEB/TFE3 DKO MEFs in response to DNA Damage
Contributors : Rosa Puertollano ; Mehdi PiroozniaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe analyze the contribution of the transcription fators TFEB and TFE3 to the DNA Damage Response (DDR) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE118517 Transcriptome analysis of control and TFEB/TFE3 DKO RAW264.7 in response to DNA Damage
Contributors : Rosa Puertollano ; Mehdi PiroozniaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe analyze the contribution of the transcription fators TFEB and TFE3 to the DNA Damage Response (DDR) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE118518 Transcriptome analysis of control and TFEB/TFE3 DKO MEFs and RAW264.7 in response to DNA Damage
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE118887 Non-coding RNA, RNY1 is essential for reprogramming process
Contributors : Daisuke Kami ; Satoshi GojoSeries Type : Expression profiling by arrayOrganism : Homo sapiensRNY1 is strongly expressed in cytoplasm during early iPS reprogramming phase (d0-3) but, underlying molecular mechanisms of RNY1 remain unknown during iPS reprogramming. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE118888 miRNA analysis of iPS reprogramming in OSKM treated TIG-1 fibroblasts on day 0 and 3.
We examined the miRNA in DDX6 antibody IP proteins during iPS reprogramming. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE118995 Integrated Multi-omic Analysis of Esthesioneuroblastomas Identifies Two Subgroups Linked to Cell Ontogeny
We report here the multi-omics analysis of esthesioneuroblastomas, which is a rare cancer arising from the olfactory bulb. We discovered ENB can be grouped in two subtypes, namely basal and neural ENBs. We also uncovered high rates of mutations (~35%) in basal ENB subgroup. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE119367 Meta-analysis Identifies MHC Loci in or near HLA-DRB1, HLA-DQA1, HLA-C as Associated with Leprosy in Chinese Han Population
Contributor : Xuelei ZhangSeries Type : Genome variation profiling by SNP arrayOrganism : Homo sapiensLeprosy is a chronic granulomatous disease caused by infection with Mycobacterium leprae. Genetic association studies indicated that leprosy risk is strongly associated with variation within the major histocompatibility complex (MHC) region, but the full number of variants in this region has yet to be elucidated. To identify further susceptibility loci or loss of function variants for this disease, we performed fine-mapping analysis of the MHC region using a Han Chinese reference panel (n= 10,689 patients, 29,948 genetic m...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Homo sapiens Source Type: research

GSE119827 RNA-seq analysis of control and NRDE2-depleted breast cancer cells
Conclusions: NRDE2 is required for suppressing intron retention in a subset of genes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120289 Profiles analysis reveals circRNAs involving zebrafish physiological development
Contributors : Heng Liu ; Yin Hu ; Jing Yin ; Xiang-Yun Yan ; Wen-Juan Chen ; Xing-Yun Wang ; Zhang-Bin Yu ; Shu-Ping HanSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Danio rerioRecent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins, modulation of transcription and interference with splicing, and even translation to produce poly-peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development, further to research the mechanism of action of circRNAs...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Danio rerio Source Type: research

GSE120595 Jarid2 Functions as a Tumor Suppressor in Myeloid Neoplasms by Repressing Self-Renewal in Hematopoietic Progenitor Cells
In this study, genetic mouse models and patient-derived xenografts (PDX) demonstrated that Jarid2 acts as a tumor suppressor in chronic myeloid disorders. Genetic deletion of Jarid2 either reduced overall survival of MPN, or drove transformation to sAML, depending on the timing and context of co-operating mutations. Mechanistically, Jarid2 recruits PRC2 to epigenetically repress self-renewal pathways in hematopoietic progenitor cells. These studies establish Jarid2 as a bona fide hematopoietic tumor suppressor and highlight new therapeutic targets. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 30, 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

GSE120659 Next Generation Sequencing Facilitates Quantitative Analysis of SMMC7721 shYTHDF2 and shCtrl transcriptomes.
Contributors : Jiajie Hou ; Zhenjun ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDynamic N6-methyladenosine (m6A) modification was previously identified as a ubiquitous post-transcriptional regulation that affected mRNA homeostasis. However, the m6A-related epitranscriptomic alterations and functions remain elusive in human diseases such as cancer. Here we show that hypoxia restrains the ‘reader’ protein YTH domain family 2 (YTHDF2), to stabilize the methylated oncogene mRNAs in inflammation-associated liver cancer. YTHDF2 silenced in human cancer cells or depleted ...
Source: GEO: Gene Expression Omnibus - September 30, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120635 KMT2B is selectively required for neuronal transdifferentiation [ChIP-seq]
Contributors : Giulia Barbagiovanni ; Pierre-Luc Germain ; Pietro Lo Riso ; Giuseppe TestaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTransdifferentiation of fibroblasts into induced Neuronal cells (iNs) by neuronal-specific transcription factors Brn2, Myt1l and Ascl1 is a paradigmatic example of inter-lineage conversion across epigenetically distant cells. Despite tremendous progress on the transcriptional hierarchy underlying transdifferentiation, the enablers of the concomitant epigenome resetting remain to be elucidated. Here we investigated the role of KMT2A and...
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE120603 RNA-sequencing of smpB-dependent gene expression in A. Veronii C4
Contributors : Zhu Liu ; Dan WangSeries Type : Expression profiling by high throughput sequencingOrganism : Aeromonas veroniiWe generated A. veronii strains that express SmpB(wt) or not( △smpB) in trans to evaluate the changes in gene expression upon SmpB expression. As SmpB participate in transtranslation sysytem, this allows us to explore the gene regulaton in A.veronii. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Aeromonas veronii Source Type: research

GSE120607 Expression data from Drosophila melanogaster wing disc - YAP/Yki vs YAP/Yki+dTcf/Pan-RNA RNAi conditions
Contributors : Shilin Song ; H éctor Herranz ; Diana AndrejevaSeries Type : Expression profiling by arrayOrganism : Drosophila melanogasterDetermine the genes controlled by dTcf/Pan involved in tumor formationmanuscript dTcf/Pangolin suppresses growth and tumor formation in Drosophila (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Drosophila melanogaster Source Type: research

GSE120611 Next Generation Sequencing Facilitates Quantitative Analysis of normal and YTHDF2 Overexpressing SMMC7721 cells in normoxia and hypoxia condition
Contributors : Jiajie Hou ; Zhenjun ZhaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDynamic N6-methyladenosine (m6A) modification was previously identified as a ubiquitous post-transcriptional regulation that affected mRNA homeostasis. However, the m6A-related epitranscriptomic alterations and functions remain elusive in human diseases such as cancer. Here we show that hypoxia restrains the ‘reader’ protein YTH domain family 2 (YTHDF2), to stabilize the methylated oncogene mRNAs in inflammation-associated liver cancer. YTHDF2 silenced in human cancer cells or depleted ...
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120612 Transcriptomic response to etoposide treatment in immune cell lines
Contributors : Sergey Nejentsev ; Olivier PapapietroSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq analysis of the effects of etoposide treatment on transcriptomes of human pre-B, mature B, T and myeloid cell lines. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120622 Fucosyltransferase 4 promotes cancer metastasis via enhancing EGFR/TGFBR signaling network and is associated with poor prognosis in non-small cell lung cancer
Conclusions: High levels of FUT4 in tumor tissues significantly correlate with poor prognosis in NSCLC patients. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120623 IKZF2 is required for myeloid leukemic stem cells by driving self-renewal and inhibiting the myeloid differentiation program II
We report that IKZF2 is required for maintaining chromatin accessibility in leukemic stem cells in myeloid leukemia. RNA seq and ATAC-seq were performed to investigate the changes in chromatin accessibility of differentially expressed genes in leukemic stem cells when IKZF2 was absent. We found that IKZF2 maintains open accessibility in self-renewal transcription factor motifs such as HOXA9 sites whereas motifs of differentiation transcription factors including C/EBPs are kept closed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE120624 Affymetrix CytoScan 750K and HD data for developmental delay and/or physical disability phenotypes samples
Contributors : Eun H Cho ; Junnam LeeSeries Type : Genome variation profiling by SNP array ; Genome variation profiling by genome tiling arrayOrganism : Homo sapiensChromosomal microdeletions/microduplications (CMM) have been associated with various neurological and developmental disorders and chromosomal microarray (CMA) is a method of choice to diagnose CMM syndromes. Recently, next-generation sequencing (NGS)-based low-coverage whole genome sequencing (LC-WGS) has been applied to detect CMM. This dataset is intended to be used as a “Golden standard data set” for development of LC-WGS analysis method. It cons...
Source: GEO: Gene Expression Omnibus - September 29, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Genome variation profiling by genome tiling array Homo sapiens Source Type: research

GSE120630 IKZF2 is required for myeloid leukemic stem cells by driving self-renewal and inhibiting the myeloid differentiation program
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - September 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE120544 Butyrivibrio hungatei MB2003 and Butyrivibrio proteoclasticus B316T grown in mono- and co-cultures on xylan or pectin
Contributors : Nikola Palevich ; Graeme T Attwood ; William J Kelly ; Jasna RakonjacSeries Type : Expression profiling by high throughput sequencingOrganism : Butyrivibrio hungatei ; Butyrivibrio proteoclasticusRumen bacterial species belonging to the genera Butyrivibrio are important degraders of plant polysaccharides, particularly hemicelluloses (arabinoxylans) and pectin. Currently, four distinct species are recognized which have very similar substrate utilization profiles, but little is known about how these microorganisms are able to co-exist in the rumen. To investigate this question, Butyrivibrio hungatei MB2003 and...
Source: GEO: Gene Expression Omnibus - September 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Butyrivibrio hungatei Butyrivibrio proteoclasticus Source Type: research