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

GSE115625 Genome-wide fork-collapse sites in MEF and MDA-MB-231 from ATR inhibition
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis 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 binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE116251 Global and targeted microRNA expression profiling in clear cell renal cell carcinoma tissues potentially links miR-155-5p and miR-210-3p to both tumorigenesis and recurrence [discovery phase]
This study aimed to profile microRNAs (miRNAs) that are dysregulated in clear cell RCC (ccRCC) tumor tissues and predictive of recurrence. The expression levels of 800 miRNAs were assessed in paired tumor and normal tissues from a discovery cohort of 18 ccRCC patients via the NanoString assay platform. MiRNAs found to be differentially expressed were further examined in a validation set of 205 patients using quantitative real-time PCR. Tumor-normal data from 64 patients in The Cancer Genome Atlas were used for external validation. Results showed 28 miRNAs were consistently dysregulated in tumor tissues. Dichotomized analys...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE116489 DNA methylation changes in Dnmt3L-deficient mouse embryonic stem cells (mESCs)
Contributors : Taiping Chen ; Hongbo ZhaoSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusWe used RRBS to analyze DNA methylation in mESC lines deficient for maternal Dnmt3L (Dnmt3L mKO), zygotic Dnmt3L (Dnmt3L KO), and both maternal and zygotic Dnmt3L (Dnmt3L mzKO). Compared to wild-type (WT) mESCs, Dnmt3L mKO mESCs exhibit severe loss of methylation at imprinted loci but no changes in global DNA methylation, Dnmt3L KO mESCs exhibit moderate loss of methylation at many Dnmt3a target regions but do not affect methylation at imprinted loci, and Dnmt3L mzKO mESCs exhibit combined change...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE118794 The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination
Contributors : Ver ónica Delgado-Benito ; Daniel B Rosen ; Qiao Wang ; Anna Gazumyan ; Joy Pai ; Thiago Y Oliveira ; Devakumar Sundaravinayagam ; Wenzhu Zhang ; Matteo Andreani ; Lisa Keller ; Kyong-Rim Kieffer-Kwon ; Aleksandra Pekowska ; Seolkyoung Jung ; Madlen Driesner ; Roman I Subbotin ; Rafael Cas ellas ; Brian T Chait ; Michel C Nussenzweig ; Michela Di VirgilioSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusClass Switch Recombination (CSR) is a DNA recombination reaction that diversifies the eff...
Source: GEO: Gene Expression Omnibus - October 4, 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

GSE120649 The Regulation of IFN Type I Pathway Related Genes RSAD2 and ETV7 Specifically Indicate Antibody-Mediated Rejection After Kidney Transplantation
Contributors : Mareen Matz ; FrederiK Heinrich ; Qiang Zhang ; Christine Lorkowski ; Kaiyin Wu ; Nils Lachmann ; Richard K Addo ; Pawel Durek ; Mir-Farzin Mashreghi ; Klemens BuddeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed total RNA-Seq and compared expression levels of genes of whole blood cells isolated from patients after kidney transplantation with stable graft function, antibody mediated- and t cell mediated graft rejection. (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

GSE120702 CRISPR activation of long non-coding RNAs transiently expressed during cortical neuron differentiation associated with Field, et al, Stem Cell Reports 2018
Contributors : Andrew R Field ; Frank M Jacobs ; Ian T Fiddes ; Alex P Phillips ; Andrea M Reyes-Ortiz ; Erin LaMontagne ; Lila Whitehead ; Vincent Meng ; Jimi L Rosenkrantz ; Mari Olsen ; Max Hauessler ; Sol Katzman ; Sofie R Salama ; David HausslerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens4 transiently expressed long non-coding RNAs that were identified in human and non-human primate cortical organoid differentiation were activated out of context in HEK293FT cells using CRISPRa. (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

GSE120756 TET2 coactivates gene expression through demethylation of enhancers
Contributors : Lu Wang ; Patrick A Ozark ; Ali ShilatifardSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Homo sapiensThe tet methylcytosine dioxygenase 2 (TET2) enzyme catalyzes the conversion of the modified DNA base 5-methylcytosine to 5-hydroxymethylcytosine. TET2 is frequently mutated or dysregulated in multiple human cancers, and loss of TET2 is associated with changes in DNA methylation patterns. Here, using newly developed TET2-specific antibodies and the estrogen respo...
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 Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120774 Expression Data from epicardial (EAT) and subcutaneous adipose tissue (SAT) in patients with coronary artery disease
Contributor : Tim FitzgibbonsSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe took samples of subcutaneous adipose tissue from the sternum (SAT) and epicardial adipose tissue (EAT) from a site adjacent to the right coronary artery in cases with coronary disease and controls without coronary disease.Cases had significant coronary disease and were undergoing coronary artery bypass surgery. Controls all had coronary angiograms and did not have significant coronary disease. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE120783 Glucocorticoid induced gene signature in human skin
Contributors : Loukia N Lili ; Anna Klopot ; Ben Readhead ; Gleb Baida ; Joel T Dudley ; Irina BudunovaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGlucocorticoids (GCs) are among the most effective and frequently prescribed anti-inflammatory drugs in dermatology. The effects of GCs are mediated by the glucocorticoid receptor (GR), a well-known transcription factor (TF). Despite the well-studied therapeutic and adverse effects of GCs, the molecular signature of GC/GR in human skin is largely unknown. Here, we present a bioinformatics analysis of the human skin transcriptome induced...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120787 Single cell RNA-sequencing of innate lymphoid cells isolated from mouse skin layers
Conclusions: This study reveals skin layer-specific transcriptomic signature of innate lymphoid cells (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

GSE120788 Control and Linc-AAM (a lincRNA associated with activated macrophages) knockdown RAW264.7 cells expression profiling under AEPS (the polysaccharide from the roots of Actinidia eriantha) stimulation
Contributors : Hongxiang Sun ; Xiangfeng Chen ; Jing DuSeries Type : Expression profiling by arrayOrganism : Mus musculusTo gain an understanding of Linc-AAM function, we performed transcriptome analysis with microarray using Linc-AAM kncockdown RAW264.7 cells or control cells with or without AEPS treatment (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120795 Atlas of RNA sequencing profiles of normal human tissues
Contributors : Anton Buzdin ; Maxim Sorokin ; Nurshat Gaifullin ; Alexey Reshetun ; Maria SuntsovaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensComprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. There is a shortage now of the gene expression data for human healthy tissues. The available data can either lack biological replicates or represent tissues adjacent to tumors removed during surgery that have signs of pathology and inflammation. For the available limited collections of normal tissues from ...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120797 Liver RNA microarray from female HDAC6 –/–, HDAC9–/– mice
Contributors : Ulf H Beier ; Tatiana Akimova ; Rongxiang Han ; Liqing Wang ; Wayne W HancockSeries Type : Expression profiling by arrayOrganism : Mus musculusWhole livers from HDAC6, HDAC9 deficient and wild type C57BL/6 mice, age 8-12 weeks, gender: female. Wild type mice with or without high fat diet (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120798 Development and Characterisation of Acquired Radioresistant Breast Cancer Cell Lines.
Conclusions: This is the first study to date that extensively describes the development and characterisation of three novel radioresistant breast cancer cell lines through both genetic and phenotypic analysis. More changes were identified between parental cells and their radioresistant derivatives in the ER+ (MCF-7 and ZR-751) compared with the ER- cell line (MDA-MB-231) model; however, multiple and likely interrelated mechanisms were identified that may contribute to the development of acquired resistance to radiotherapy. (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

GSE120800 Differentially expressed (DE) genes analysis in synovial fluid mesenchymal stem cells (SF-MSCs), SF-MSC derived iPSCs and iPSC derived MSCs (iPSC-MSCs)
We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:SF-MSCs, iPSCs and iPSC-MSCs. Our results shown that iPSC-MSCs were more similar to SF-MSCs than iPSCs. (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

GSE120804 Molecular Characterization of a Precision-Cut Rat Liver Slice Model for the Evaluation of Anti-Fibrotic Compounds
In this study using RNAquencing we demonstrated that various pathways functionally related to fibrotic mechanisms were dysregulated in PCLSs derived from rats subjected to bile duct ligation. The Alk5 inhibitor SB525334, nintedanib and sorafenib each reversed a subset of genes dysregulated in fibrotic PCLSs and of those genes we identified 608 genes whose expression was reversed by all three compounds. These genes define a molecular signature characterizing many aspects of liver fibrosis pathology and its attenuation in the model. A panel of 12 genes and 4 secreted biomarkers including procollagen I, HA, IGFBP5 and WISP1, ...
Source: GEO: Gene Expression Omnibus - October 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE120772 Gene expression patterns of trisomy 12 hPSC lines
Contributors : Yohei Hayashi ; Miho K FurueSeries Type : Expression profiling by arrayOrganism : Homo sapiensTrisomy 12 disrupts the genome-wide expression patterns that are required for proper mesendodermal differentiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE102069 Unraveling cis-regulatory elements by mapping structural changes in mRNAs
Contributors : Orel Mizrahi ; Alina Shitrit ; Idit Gilbert ; Aharon Nachshon ; Noam Stern-GinossarSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensmRNA molecules are generally thought to be messengers of genetic information in the cell. Stretches of RNA that are complementary in sequence have a propensity to pair, forming elements of secondary structure within RNA molecules. Although these structures will exist in every mRNA molecule, the role they play in gene regulation is not well understood. Currently two techniques are available to profile the cell RNA structure, in-vivo, ...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE111878 The m 6 A-methylase complex recruits TREX and regulates mRNA export.
Contributors : Simon Lesbirel ; Nicolas Viphakone ; Matthew Parker ; Jacob Parker ; Catherine Heath ; Ian Sudbery ; Stuart A WilsonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensN6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modification has previously been shown to alter the export kinetics for mRNAs though the molecular details surrounding this phenomenon remain poorly understood. Here we show that the m6A complex (WTAP, KIAA1429, METTL3/14) drives recruitment of the TREX mRNA export complex onto m6A modified mRNAs and this process is e...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE119435 Tight regulation of hippocampal functions by prolactin
Contributors : Erika A Cabrera-Reyes ; Mauricio Rodr íguez-Dorantes ; Edgar R Vázquez-Martínez ; Nadia A Rivero-Segura ; Omar Collazo-Navarrete ; América Vanoye–Carlo ; Marco CerbónSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusProlactin is a pleiotropic hormone with multiple functions in several tissues and organs, including the brain, in which is exerts neuroprotective effects against excitotoxicity in the hippocampus. However, the molecular mechanisms involved in the actions of PRL in the hippocampus have not been fully elucidated. The...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE119655 Small is big in Arabidopsis mitochondrial ribosome
Contributors : Tan-Trung Nguyen ; Hakim MireauSeries Type : OtherOrganism : Arabidopsis thalianaMitochondria are responsible for energy production through aerobic respiration and represent the powerhouse of eukaryotic cells. Their metabolism and gene expression processes combine bacterial-like features and traits that evolved in eukaryotes. Among mitochondrial gene expression processes, translation remains the most elusive. In plants, while numerous pentatricopeptide repeat (PPR) proteins are involved in all steps of gene expression, their function in translation remains unclear. Here we present the biochemical characteris...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Other Arabidopsis thaliana Source Type: research

GSE120726 The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels
Contributors : Yin Xuefeng ; Orr Mona ; Wang Hanbo ; Hobbs Errett ; Shabalina Svetlana ; Storz GiselaSeries Type : Expression profiling by arrayOrganism : Escherichia coli ; Escherichia coli str. K-12 substr. MG1655In response to low levels of magnesium (Mg2+), the PhoQP two component system induces the transcription of two convergent genes, one encoding a 31-amino acid protein denoted MgtS and the second encoding a small, regulatory RNA (sRNA) denoted MgrR. Previous studies showed that the MgtS protein interacts with and stabilizes the MgtA Mg2+ importer to increase intracellular Mg2+ levels, while the MgrR sRNA base pair...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Escherichia coli Escherichia coli str. K-12 substr. MG1655 Source Type: research

GSE120731 The Scalloped and Nerfin-1 transcription factors cooperate to maintain neuronal cell fate
Contributors : Jan Schroeder ; Joseph H Vissers ; Francesca Froldi ; Anthony Papenfuss ; Louise Y Cheng ; Kieran F HarveySeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Drosophila melanogasterThe ability of cells to stably maintain their fate is governed by specific transcription regulators. Here, we show that the Scalloped (Sd) and Nervous fingers-1 (Nerfin-1) transcription factors physically and functionally interact to maintain medulla neuron fate in the Drosophila melanogas...
Source: GEO: Gene Expression Omnibus - October 3, 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 Drosophila melanogaster Source Type: research

GSE120733 β-cryptoxanthin enhanced peripheral leukocyte functions, and transcriptomes of the peripheral neutrophil and liver in Holstein cattle
Contributors : Keiichiro Kizaki ; Yo-Han KimSeries Type : Expression profiling by arrayOrganism : Bos taurusWe investigated the effect of oral administration of β-CRX on its serum concentration, peripheral leukocyte functions, and transcriptomic dynamics of the peripheral neutrophil and liver tissue in Holstein cattle. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Bos taurus Source Type: research

GSE120734 mRNA-seq for etoposide-treated TLP-knockdown cells
Contributors : Hidefumi Suzuki ; Yuki YamaguchiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe explored the mechanism by which TLP affects DNA damage response. We performed mRNA-seq analysis of non-treated and etoposide-treated samples in control and TLP-knockdown cells. We show that TLP is critical for global transcriptional repression after double-strand DNA breaks (DSBs). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120736 Comprehensive molecular classification of bladder cancer reveals distinct prognostic subgroups with different sensitivities to immunotherapy
This study aimed to identify distinct molecular subtypes of BC and the clinical and/or biological characteristics of each subtype. We used seven gene expression data sets for bladder cancer, which included data from 118 primary bladder cancer samples and 27 recurrent bladder tumor tissues from the Yonsei University Severance Hospital. Hierarchical clustering revealed four molecular subtypes of BC with different clinical outcomes: class 1 with low-grade NMIBC and the best prognosis; class 2 characterized by active FGFR3 and inhibited immune response pathways; class 3 with high-grade NMIBC and the worst progression-free surv...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE120737 Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy [WT vs. Tg]
Contributors : Qing-jun Zhang ; Zhi-ping LiuSeries Type : Expression profiling by arrayOrganism : Mus musculusHeart disease and failure is a leading cause of mortality worldwide. Left ventricular hypertrophy (LVH) and myocardial fibrosis are the major risk factor for cardiovascular morbidity and mortality and the development of heart failure. Pathological LVH induced by sustained pressure-overload engages transcriptional programs including reactivation of canonical fetal genes and those inducing fibrosis. Histone lysine demethylases (KDMs) are emerging potent regulators of transcriptional reprogramming in cancer, though th...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120738 Integrative epigenetic taxonomy of primary prostate cancer [ChIP-Seq]
We present a rich novel resource on transcriptional and epigenetic control in prostate cancer, revealing a tight control of gene regulation differentially dictated by AR over the three subtypes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120739 Kdm3a in mouse promotes pressure overload induced cardiac hypertrophy [WT vs. KO]
Contributors : Qing-jun Zhang ; Zhi-ping LiuSeries Type : Expression profiling by arrayOrganism : Mus musculusHeart disease and failure is a leading cause of mortality worldwide. Left ventricular hypertrophy (LVH) is a major risk factor for cardiovascular morbidity and mortality and the development of heart failure. Pathological LVH induced by sustained pressure-overload engages transcriptional programs including reactivation of canonical fetal genes and those inducing fibrosis. Histone lysine demethylases (KDMs) are emerging potent regulators of transcriptional reprogramming in cancer, though their potential role in abnor...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120741 Integrative epigenetic taxonomy of primary prostate cancer [RNA-Seq]
We present a rich novel resource on transcriptional and epigenetic control in prostate cancer, revealing a tight control of gene regulation differentially dictated by AR over the three subtypes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120742 Integrative epigenetic taxonomy of primary prostate cancer
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 3, 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

GSE120754 Impact of two reoviruses and their coinfection on the rice RNAi system and vsiRNA production
This study revealed that both SRBSDV and RRSV affect the RNA interference (RNAi) pathway and form different virus-derived interfering RNA (vsiRNA) profiles in rice. Co-infection of rice by SRBSDV and RRSV up-regulated the expression of rice Dicer and DICER-like (DCL) proteins but down-regulated the expression of rice RNA-dependent RNA polymerases (RDRs), and the accumulation of vsiRNAs of either RBSDV or RRSV was decreased compared with that in singly infected plants. The majority of SRBSDV vsiRNAs were 21 nt or 22 nt in length, whether plants were singly infected with SRBSDV or co-infected with RRSV. On the other hand, th...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE120760 Expression profiling of Pseudomonas aeruginosa in chronic wound exudate media
Contributors : Philip S Stewart ; Ben White ; Laura Boegli ; Timothy Hamerly ; Kerry S Williamson ; Michael J Franklin ; Brian Bothner ; Garth A James ; Steve Fisher ; Francisco G Vital-Lopez ; Anders WallqvistSeries Type : Expression profiling by arrayOrganism : Pseudomonas aeruginosaTranscriptomic, metabolomic, physiological, and computational modeling approaches were integrated to gain insight into the mechanisms of antibiotic tolerance in an in vitro biofilm system. Pseudomonas aeruginosa biofilms were grown in drip-flow reactors on a medium composed to mimic the exudate from a chronic wound (CWE). After 72 hours, the ...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Pseudomonas aeruginosa Source Type: research

GSE120763 Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - human
Contributors : Darya Vanichkina ; Anupma ChoudharySeries Type : OtherOrganism : Homo sapiensMicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify m icroRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel meth...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE120764 Identification of miR-29b targets using 3-cyanovinylcarbazole containing mimics - mouse
Contributors : Darya Vanichkina ; Anupma ChoudharySeries Type : OtherOrganism : Mus musculusMicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify m icroRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel meth...
Source: GEO: Gene Expression Omnibus - October 3, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research