GSE114210 IG-MYC-positive neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas
Contributors : Siebert Reiner ; Wagener RabeaSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome wide DNA methylation profiling of Burkitt lymphoma subsets. The Illumina Infinium HumanMethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 85,000 CpGs in B-cell lymphoma samples. Samples included 2 primary IG-MYC-positive B-cell neoplasms with precursor B-cell phenotype and 5 Burkitt lymphoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE114820 A Transcriptomic Analysis of the Development of Skeletal Muscle Atrophy in Cancer-Cachexia in Tumor-Bearing Mice
Contributor : Nicholas GreeneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe recently demonstrated mitochondrial degenerations precede muscle wasting in time course progression of CC. However, the extent of muscle perturbations prior to wasting in CC is unknown. Therefore, we performed global gene expression analysis in CC-induced muscle wasting to enhance understanding of intramuscular perturbations across the development of CC. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE115024 MYC interacts with the G9a histone methyltransferase to drive transcriptional repression and tumorigenesis
Contributors : William B Tu ; Yu-Jia Shiah ; Paul C Boutros ; Linda Z PennSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMYC is an oncogenic driver that regulates transcriptional activation and repression, yet molecular mechanisms of MYC transformation remain unclear. We demonstrate that MYC interacts with the G9a H3K9-methyltransferase complex to control transcriptional repression. Inhibiting G9a hinders MYC chromatin binding at MYC-repressed genes and de-represses gene expression to antagonize cellular transformation. By identifying the MYC Box II region as essential for MYC-G9a in...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116016 Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase
Contributors : Emily K Schutsky ; Hao Wu ; Rahul M KohliSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusHere we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold l...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE116453 Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing
In this study, we established a molecularly-barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 E. coli cell culture samples were defined with a high confidence (P
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Escherichia coli ATCC 8739 Source Type: research

GSE118299 Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [AGO2-RIP-Seq]
Contributors : Volker Busskamp ; Lisa K Kutsche ; Joerg Fallmann ; Mathias Lesche ; Andreas DahlSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensNon-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 is assigned as a key player of neuronal differentiation via its complex, but little understood, regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human stem cells. Upon neuronal induction, miR-124-depleted cells underwent ne...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118302 Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [AGO2-RIP-Seq -miRNAs]
Contributors : Volker Busskamp ; Lisa K Kutsche ; Joerg Fallmann ; Mathias Lesche ; Andreas DahlSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNon-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 is assigned as a key player of neuronal differentiation via its complex, but little understood, regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human stem cells. Upon neuronal induction, miR-124-depleted cells underwent neurog...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118307 Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [Timecourse RNA-Seq]
Contributors : Volker Busskamp ; Lisa K Kutsche ; Deisy M Gysi ; Mathias Lesche ; Andreas DahlSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNon-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 is assigned as a key player of neuronal differentiation via its complex, but little understood, regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human stem cells. Upon neuronal induction, miR-124-depleted cells underwent neurogen...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118310 Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [d7+d14]
Contributors : Volker Busskamp ; Lisa K Kutsche ; Deisy M Gysi ; Mathias Lesche ; Andreas DahlSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNon-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-124 is assigned as a key player of neuronal differentiation via its complex, but little understood, regulation of thousands of annotated targets. To systematically chart its regulatory functions, we used CRISPR/Cas9 gene editing to disrupt all six miR-124 alleles in human stem cells. Upon neuronal induction, miR-124-depleted cells underwent neurogen...
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118316 Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.
Series Type : Non-coding RNA profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120094 Role of Hac1 in unfolded protein response in Candida parapsilosis
Contributors : Mihaela Ola ; Elise Iracane ; Paul Donovan ; Linda Holland ; Geraldine ButlerSeries Type : Expression profiling by high throughput sequencingOrganism : Candida parapsilosisInvestigation of the role of HAC1 using transcriptional profiling of Candida parapsilosis treated with 5 mM dithiothreitolGene expression of wild type and hac1 deletion strains were compared during growth in YPD only and growth in YPD with 5 mM DTT (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Candida parapsilosis Source Type: research

GSE120844 Pomalidomide inhibits PD-L1 induction to promote anti-tumor immunity
We examined genome-wide how pomalidomide affects IFN-gamma-induced PD-L1 expression in human melanoma cell line. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 8, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106371 Transcriptome of zebrafish neurohypophyseal astroglia (pituicytes)
Contributors : Dena Leshkowitz ; Savani Anbalagan ; Gil LevkowitzSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe hypothalamo-neurohypophyseal system (HNS) is an interface through which the brain regulates body homeostasis by means of releasing the hypothalamic neurohormones oxytocin and arginine-vasopressin to the general circulation. The basic components of the HNS are the hypothalamic axonal projections, endothelial blood vessels and astroglial-like cells, termed pituicytes. These three tissue types converge and interact at the ventral forebrain to establish an efficient neuro-va...
Source: GEO: Gene Expression Omnibus - October 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE73919 Global changes of gene expression inuced by MIR31HG knockdown
Contributor : Yongsheng ZhouSeries Type : Expression profiling by arrayOrganism : Homo sapiensHuman adipose-derived stem cells (hASCs) are a highly attractive source in bone tissue engineering.We found that MIR31HG significantly promote the osteogenic differentiation of hASCs. However, the underlying mechanisms still await investigations. Thus the alteration of gene expression induced by MIR31HG knockdown was investigated.We used microarrays to detail the global programme of gene expression when MIR31HG was knocked down in hASCs and identified distinct classes of dn-regulated genes during this process. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE97552 Comparative gene expression of CD34+ human hematopoietic progenitor cells upon knockdown of STAT5
The objective of the study is to identify the genes regulated by STAT5 in very primitive human hematopoietic stem progenitor cells (HSPCs). We used Affymetrix Human Genome U133 Plus 2.0 microarrays to investigate gene expression in human CD34+CD38- HSPC upon expression of STAT5 or control luciferase shRNA-encoding vectors. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE120904 Specific targeting of the common gamma chain blocks cooperative reprogramming of human tissue-resident cytotoxic T lymphocytes by IL-15 and IL-21
Contributors : Ciszewski Cezary ; Discepolo Valentina ; Pacis Alain ; Doerr Nick ; Maglio Mariantonia ; Basheer Asjad ; Al-Mawsawi Laith ; Troncone Riccardo ; Azimi Nazli ; Tagaya Yutaka ; Barreiro Luis ; Jabri BanaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe common gamma chain ( γc) is required for productive signaling by interleukin (IL)-15, IL-21 and IL-2, which are critically involved in immune activation and regulation. IL-21 and IL-15 are implicated in the pathogenesis of type-1 diabetes, graft-versus-host disease, and celiac disease (CeD), a gluten-mediated autoimm...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE87670 Pathogen size alters C-type lectin receptor signaling in dendritic cells to influence CD4 T cell differentiation
In this study we show that when dendritic cells encounter pathogens that are too large to internalize, or when phagocytosis of small microbes is blocked, dendritic cells adopt an activation profile that allows them to orchestrate an adaptive immune response commonly associated with tissue repair and anti-helminth immunity. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104692 Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish (Danio rerio) progeny
This study shows that the dietary n-3/n-6 PUFA ratio can alter gene expression patterns in the adult progeny. Whether the effe ct is mediated by permanent epigenetic mechanisms regulating gene expression in developing gametes needs to be further investigated. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE104921 Signal integration in lymphocytes via convergent genomic actions of NFATs with IRF4 and IRF8
Contributors : Ankur Saini ; Jeremy Riddell ; Masashi Yukawa ; Artem Barski ; Matthew T Weirauch ; Harinder SinghSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusLymphocyte activation and effector state differentiation critically depend on integration of multiple signals, including those from antigen, co-stimulatory ligand and cytokine receptors. Thus, discovery of molecular components and mechanisms underlying signal integration is vital for the understanding and control of adaptive immune responses. Sti...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE106881 Spliceosome specifically associates with RNA polymerase II CTD Ser5-P isoform to promote co-transcriptional splicing
Contributors : Takayuki Nojima ; Kenny Rebelo ; Tom ás Gomes ; Ana Rita Grosso ; Nicholas J Proudfoot ; Maria Carmo-FonsecaSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusCo-transcriptional splicing of introns is a defining feature of eukaryotic gene expression. We show that the mammalian spliceosome specifically associates with the S5P CTD isoform of RNA polymerase II (Pol II) as it elongates across spliced exons of protein coding genes, both in human Hela and murine lymphoid cell lines. Immuno-precipitation of MNase digested chromatin with phospho CTD s...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Mus musculus Source Type: research

GSE112836 The effects of IIS/TOR signaling on gene expression in Drosophila males and females: IIS/TOR impacts sex-differential gene expression
Contributors : Rita M Graze ; Michelle N ArbeitmanSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterThe insulin signaling pathway is known to interact directly and indirectly with the sex determination regulatory hierarchy, playing a role in directing sexually dimorphic traits. To understand the degree to which the insulin signaling pathway contributes to sexually dimorphic gene expression in adult animals, we examined the effect of perturbation of the pathway on gene expression in male and female Drosophila. Our data reveal a large effect of insulin signaling on expression i...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE113090 Deep sequencing of transcript levels of human embryonic stem cell derived mesothelium (epithelial and mesenchymal forms) and mesothelium from neonatal mouse E15.5 of the heart, lung, liver and gut and ChIP-seq data of the mesenchymal form of mesothelium
Contributors : Stephen Dalton ; Thomas Colunga ; Miranda Hayworth ; Luoman Chen ; Kristopher L NazorSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusMesothelium is a multipotent resident progenitor cell of the coelomic organs that functions in organogenesis, repair and possible regeneration. We used hESCs to generate mesothelium of the epithelial and mesenchymal forms. Mesenchymal derivatives of mesothelium have been previously reported to function in tissue repair by promoting and participating in angiog...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE116754 Methylation analysis of human embryonic stem cells (hESCs), hESC-derived splanchnic mesoderm and hESC-derived mesothelium (mesenchymal form)
Contributors : Jeanne Loring ; Kristopher L Nazor ; Stephen Dalton ; Miranda Hayworth ; Thomas ColungaSeries Type : Methylation profiling by array ; Third-party reanalysisOrganism : Homo sapiensGenome wide DNA methylation profiling of hESC-derived mesothelium (MesoT), hESCs and hESC-derived splanchnic mesoderm (SplM) compared to primary human tissue samples. The Illumina Infinium HumanMethylation450 BeadChip kit was used to obtain DNA methylation profiles across approximately 450,000 methylation sites. Samples include 2 WA09 hESCs, 2 hESC-derived splanchnic mesoderm and 3 hESC-derived mesothelium replicates. (Source: GEO: ...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Third-party reanalysis Homo sapiens Source Type: research

GSE120870 Gene expression in microdissected embryonic regions during mouse axis elongation.
Contributors : Filip J Wymeersch ; Stavroula Skylaki ; Yali Huang ; Julia A Watson ; Constantinos Economou ; Carylyn Marek-Johnston ; Simon R Tomlinson ; Valerie WilsonSeries Type : Expression profiling by arrayOrganism : Mus musculusThis dataset contains spatiotemporal transcriptome information on different axial progenitors throughout mouse axis elongation. Neuromesodermal Progenitors (NMPs), Lateral and Paraxial Mesoderm Progenitors (LPMPs), and Notochord Progenitors (NotoPs) show distinct expression profiles. Extensive similarity between NMPs and their immediate mesoderm-committed descendants at each stage investigated...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120877 Bacterial sepsis triggers an antiviral response that causes translation shutdown
Contributor : Takashi HatoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn response to viral pathogens, the host upregulates antiviral genes that suppress translation of viral mRNAs. However, induction of such antiviral responses may not be exclusive to viruses as the pathways lie at the intersection of broad inflammatory networks that can also be induced by bacterial pathogens. Using a model of Gram-negative sepsis, we show that propagation of kidney damage initiated by a bacterial origin ultimately involves antiviral responses that result in host translation shutdown. We determine...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120879 Transcriptomic profiling of S2/S3 proximal tubules in response to LPS treatment
Contributors : Takashi Hato ; Pierre C DagherSeries Type : Expression profiling by arrayOrganism : Mus musculusTo investigate the mechanisms of endotoxin-mediated kidney injury as well as renoprotective effects of endotoxin preconditioning, we performed manual microdissection of S2/S3 proximal tubules in mice as follows: 1) Non-preconditioned mice subjected to single-dose 5 mg/kg LPS (0111:B4) i.p. for 4 hrs. 2) Non-preconditioned mice subjected to single-dose 5 mg/kg LPS (0111:B4) for 24 hrs. 3) Preconditioned mice subjected to 0.25 mg/kg LPS followed 24 hour later by 5 mg/kg LPS for 4 hrs. 4) Preconditioned mice subjecte...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120885 Inherent DNA binding specificities of the HIF-1 α and HIF-2α transcription factors in chromatin (ChIP-seq)
Contributor : David R MoleSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHypoxia inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-a isoforms, HIF-1a and HIF-2a, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1b to activate a broad range of transcriptional responses. Here we report on the pan-genomic distribution of isoform-specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF-a isoform. Our findi...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120886 Inherent DNA binding specificities of the HIF-1 α and HIF-2α transcription factors in chromatin (RNA-seq)
Contributor : David R MoleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHypoxia inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-a isoforms, HIF-1a and HIF-2a, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1b to activate a broad range of transcriptional responses. Here we report on the pan-genomic distribution of isoform-specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF-a isoform. Our findings reveal tha...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120887 Inherent DNA binding specificities of the HIF-1 α and HIF-2α transcription factors in chromatin
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120888 RNA-seq tumor immunome analysis of murine breast cancer model EMT6-hHER2 responsive to novel antibody drug conjugate T-PNU
Contributors : Ulrike Menzel ; Lucia D'Amico ; Michael PrummerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAn orthotopic murine breast cancer model was created by transfecting the human HER2 gene into the breast cancer cell line EMT6 resulting in EMT6-hHER2. Previous in vivo tumor treatments with trastuzumab, trastuzumab-emtansine (T-DM1) and a novel antibody drug conjugate (ADC) T-PNU (provided by NBE therapeutics and carrying the highly potent anthracycline analogue PNU-159682) revealed that EMT6-hHER2 tumors are unresponsive to standard therapy treatments of trastuzumab and T-DM...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120892 Altered binding of tumor antigenic peptides to MHC class I affects CD8 T cell effector responses
Contributors : Eleanor Clancy-Thompson ; Christine A Devlin ; Paul M Tyler ; Mariah M Servos ; Lestat R Ali ; Katherine S Ventre ; M A Bhuiyan ; Patrick T Bruck ; Michael E Birnbaum ; Stephanie K DouganSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusT cell priming occurs when a na ïve T cell recognizes cognate peptide-MHC complexes on an activated antigen presenting cell. The circumstances of this initial priming have dramatic ramifications on the fate of the newly primed T cell. Newly primed CD8 T cells can embark onto different trajectories, with some becoming short lived effec...
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120894 SOX4 binding profiling in mouse embryonic neural stem cells (NSCs)
Contributors : L Braccioli ; S Vervoort ; P J CofferSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusBy chromatin-immunoprecipitating (ChIP) SOX4 in NSCs we identified genome-wide binding sites for SOX4 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE120899 A Phase 2 Randomized Trial of Apremilast in Patients With Atopic Dermatitis
Contributors : Eric Simpson ; Shinichi Imafuku ; Yves Poulin ; Benjamin Ungar ; Lisa Zhou ; Kunal Malik ; Huei-Chi Wen ; Hui Xu ; Yeriel D Estrada ; Xiangyu Peng ; Mindy Chen ; Nilam Shah ; Mayte Suarez-Farinas ; Ana B Pavel ; Kristine Nograles ; Emma Guttman-YasskySeries Type : Expression profiling by arrayOrganism : Homo sapiensA phase 2, double-blind, placebo-controlled trial evaluated apremilast efficacy, safety, and pharmacodynamics in adults with moderate to severe atopic dermatitis (AD). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE120805 RNA-Seq analysis of human lens epithelial cells exposed to ionizing radiation
Conclusion: Overall, the results suggest that radiation induces complex non-linear transcriptional dose-response relationships that are dose-rate dependent. Pathways shared between the two dose rates may be important contributors to radiation-induced cataractogenesis. BMD analysis suggests that the majority of pathways are activated above 0.6 Gy, which supports current ICRP identified dose thresholds for deterministic effects to the lens of the eye of 0.5 Gy. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE73722 Comparative transcriptome analysis in induced neural stem cells reveals defined neural cell identities in vitro and after transplantation into the adult rodent brain
Contributors : Anna-Lena Hallmann ; Christina Zerfass ; Marcos J Ara úzo-Bravo ; Volker Senner ; Marc Ehrlich ; Olympia E Psithaki ; Don-Wok Han ; Natalia Tapia ; Holm Zaehres ; Hans R Schöler ; Tanja Kuhlmann ; Gunnar HargusSeries Type : Expression profiling by arrayOrganism : Mus musculusReprogramming technology enables the production of large quantities of neural progenitor cells (NPCs) from somatic cells by direct transdifferentiation.However, little is known on how neural programs in these neural stem cells (iNSCs) differ from those of alternative stem cell populations in vitro and in vivo.Here, we perform...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE77985 Transcriptomic basis for reinforcement of elm anti-herbivore defense mediated by insect egg deposition
In this study we applied RNA-sequencing to a set of larvae-challenged elm trees that had either been untreated before or been exposed to prior egg deposition by elm leaf beetles. This dataset allowed us to characterize the global transcriptional response of egg-primed and non-primed elm trees at different time points after the priming stimulus itself and after the onset of larval feeding. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Ulmus minor Source Type: research

GSE92904 Genetic analysis of isoform usage in the human anti-viral response
Contributors : Chun J Ye ; Jenny Chen ; Alexandra-Chlo é Villani ; Meena Subramaniam ; Rachel E Gate ; Tushar Bhangale ; Mark N Lee ; Towfique Raj ; Raktima Raychowdhury ; Weibo Li ; Noga Rogel ; Sean Simmons ; Selina H Imboywa ; Portia I Chipendo ; Cristin McCabe ; Michelle H Lee ; Irene Y Frohlich ; Barbara E Stranger ; Philip L De Jager ; A viv Regev ; Tim Behrens ; Nir HacohenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhile genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternativ...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE94446 Gene expression in Arabidopsis leaves after P. brassicae egg deposition and/or herbivory by P. brassicae larvae
Contributors : Vivien Firtzlaff ; Jana Oberl änder ; Monika Hilker ; Reinhard KunzeSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaPlants can prepare their defense of impending herbivory, when they previously perceived eggs deposited by herbivores insect which reliably indicates that larvae will soon hatch and feed on the plants. Using Arabidopsis thaliana and Pieris brassicae we addressed the question whether prior egg deposition affects transcriptional changes in feeding-damaged plants. We determined the transcriptomes of Arabidopsis leaves that (i) were for six days deposited with eggs and...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE100790 Genome-wide fork-collapse sites in MEFs from ATR inhibition
Contributors : Nishita K Shastri ; Yu-Chen Tsai ; Eric J BrownSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTransient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which suppresses fork breakage, strand resection, and RPA accumulation. Herein, we use RPA ChIP-Seq to identify replication-problematic loci (RPLs) across the mammalian genome from ATR inhibition. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE101107 Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [ARRAY]
Contributors : Hanna Engqvist ; Toshima Z Parris ; Elisabeth Werner R önnerman ; Elin M Söderberg ; Jana Biermann ; Claudia Mateoiu ; Karin Sundfeldt ; Anikó Kovács ; Per Karlsson ; Khalil HelouSeries Type : Genome variation profiling by SNP arrayOrganism : Homo sapiensOvarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for early-stage (...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Homo sapiens Source Type: research

GSE101108 Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival [RNA-Seq]
Contributors : Hanna Engqvist ; Toshima Z Parris ; Elisabeth Werner R önnerman ; Elin M Söderberg ; Jana Biermann ; Claudia Mateoiu ; Karin Sundfeldt ; Anikó Kovács ; Per Karlsson ; Khalil HelouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOvarian cancer is the most lethal gynecological malignancy in the western world. Despite recent efforts to characterize ovarian cancer using molecular profiling, few targeted treatment options are currently available. Here, we examined genetic variants, fusion transcripts, SNP genotyping, and gene expression patterns for ea...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE101109 Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival
Series Type : Genome variation profiling by SNP array ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by SNP array Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE106851 Landscape of H3K4me3 in human CD19 cells
Contributors : Amy Leung ; Dustin E SchonesSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensChromatin immunoprecipiation of H3K4me3 of isolated B cells from healthy human donors and LCLs and RNA-sequencing of extracted RNAs (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE107966 Unliganded Progesterone Receptor Governs Estrogen Receptor Gene Expression by Regulating DNA Methylation in Breast Cancer Cells
Contributors : Gaetano Verde ; Lara I De Llobet ; Roni H Wright ; Javier Quilez ; Sandra Peir ó ; François Le Dily ; Miguel BeatoSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensHow breast cancers respond to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively), with doublenegative ER-/PR- breast cancers having worse clinical outcome than ER+/PR+ breast cancers. Although much is known about ER α gene (ESR1) regulation after hormonal stimulation, how it is regulated in the absence of hormones is not...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112506 RNA-sequencing of mouse thymic leukemias extracted from Mb1-CreDPB mice
We examined the patterns of gene expression of mouse thymic leukemias extracted from Mb1-CreDPB mice by RNA sequencing (RNA-seq). Our goal was to integrate RNA-seq data with whole-exome sequencing (WES) to determined secondary driver mutations of leukemogenesis in the absence of Spi-B and PU.1, (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112623 Optimal settings of mass spectrometry open search strategy for higher confidence
Contributors : Shaohua Lu ; Zhibiao MaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMore than half of the mass spectra could not be identified in most proteome mass spectrometry experiments. Various modifications have been considered as a major reason. Open search strategy was then introduced to solve this problem, however, lacking thorough quality assessment using independent information. Here, we used the “Suspicious Discovery Rate (SDR)” based on the translatome sequencing (RNC-seq) as an independent source to assess the proteome open search strategy. We found that t...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113111 sc-RNA sequencing of skeletal muscle macrophages during T. gondii infection and injury
Contributors : Richard M Jin ; Elizabeth A WohlfertSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe proper coordination of macrophages is essential for skeletal muscle repair. However, the full heterogenity of macrophages responding to injury has yet to be elucidated on the single-cell level. Furthermore, chronic inflammation may shift macrophage heterogeneity at steady-state and affect the generation of heterogeneity necessary for tissue repair. We use scRNA-sequencing to determine the heterogeneity of skeletal muscle macrophages during infection and wound repair (uninfected and i...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114041 Gene expression in Arabidopsis leaves after P. brassicae egg deposition
Contributors : Vivien Firtzlaff ; Monika Hilker ; Reinhard KunzeSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaCharacterization of Arabidopsis thaliana`s transcriptional response to Pieris brassicae eggs (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE115623 Genome-wide fork-collapse sites in MDA-MB-231 cells from ATR inhibition [human]
Contributors : Nishita K Shastri ; Eric J BrownSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTransient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which suppresses fork breakage, strand resection, and RPA accumulation. Herein, we use a developed DNA break-detection assay, BrITL, to identify replication-problematic loci that become processed into persistent double-strand breaks across the human genome from ATR inhibition. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115624 Genome-wide fork-collapse sites in MEFs from ATR inhibition [mouse]
Contributors : Nishita K Shastri ; Eric J BrownSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTransient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which suppresses fork breakage, strand resection, and RPA accumulation. Herein, we use a developed DNA break-detection assay, BrITL, to identify replication-problematic loci (RPLs) that become processed into persistent double-strand breaks across the mammalian genome from ATR inhibition. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research