Contributors : Simona Seizova ; Chris J Tonkin ; Alexandra L GarnhamSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Toxoplasma gondiiThe purpose of this data set is to determine if bradyzoites impact the host transcripton in a similar manner as tachyzoites. We found that 3853 differentially expressed genes (DEGs) are shared between tachyzoite infected cells and bradyzoite infected cells (41%; 2161 up-reg., 1692 down-reg.) when compared to uninfected host...
2h
Contributors : Anne-Laure Mahul-Mellier ; Marion LeleuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusParkinson’s disease (PD) is characterized by the accumulation of misfolded and aggregated alpha-synuclein (α-syn) into intraneuronal inclusions named Lewy bodies (LB). Although it is widely believed that α-syn plays a central role in the pathogenesis of PD, the processes that govern α-syn fibrillization and LB formation remain poorly understood. In this work,...
2h
Contributors : Donald J Zack ; David M GammSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPhotoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degeneration are not well understood. Treatment strategies would benefit from an improved understanding of gene-expression patterns directing photoreceptor development, as many genes are implicated in both development and degeneration. Neural retina leucine zipper (NRL) is critical...
2h
Contributors : Tayyaba Jiwani ; Norman RosenblumSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTranscriptional profiling to identify genes differentially regulated by Sufu during cerebellum development. Sufu was specifically deleted from the granule neuron compartment using Math1-driven Cre recombinase.
2h
Contributors : Buqing Ye ; Benyu LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe previously demonstrated that SRCAP regulates the self-renewal of ESCs and modulates lymphoid lineage commitment. We further validated that SRCAP was mainly distributed in liver, spleen and intestine by Northern blot. SRCAP was also highly expressed in Lgr5+ ISCs. We then sought to explore the physiological role of SRCAP in the regulation of self-renewal maintenance of ISCs.We...
2h
Contributors : Virginie Dubourg ; Alexander Nolze ; Michael Kopf ; Michael Gekle ; Gerald SchwerdtSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOchratoxin A (OTA) is a nephrotoxin that has been associated with kidney damages. The goal of this project was to identified which impact had nanomolar concentrations of this toxin on cells derived from human kidney in order to identify putative key regulators and underlying mechanisms of the already described...
2h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Jason R Plemel ; V W YongSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFollowing all types of neurological injury, resident macrophages are activated locally, and blood-derived macrophages are recruited. Distinguishing the role of resident and blood-derived macrophages is complicated by the difficulty in distinguishing between these cell types because they mostly express the same molecular markers in a diseased state. To begin to understand...
2h
Contributors : Bérengère de Laval ; Julien Maurizio ; Orit Matcovitch-Natan ; Eyal David ; Ido Amit ; Sandrine Sarrazin ; Michael H SiewekeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHere we show that immune challenge can induce epigenetic memory in HSC. We show that LPS, a gram-negative bacterial component, induces changes in HSC differentiation and gene expression that returned rapidly to normal but also establish novel open chromatin regions (OCR)...
2h
Contributors : Kazuhide Watanabe ; Imad Abugessaisa ; Masataka Takahashi ; Harukazu Suzuki ; Takeya KasukawaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAnalysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised with the presence of poor quality cells. For meaningful analyses, such poor quality cells should be excluded before detailed analysis. However, there exist no clear guidelines. Here we introduce SkewC a...
2h
Contributors : Bérengère de Laval ; Julien Maurizio ; Orit Matcovitch-Natan ; Eyal David ; Ido Amit ; Sandrine Sarrazin ; Michael H SiewekeSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHere we show that immune challenge can induce epigenetic memory in HSC. We show that LPS, a gram-negative bacterial component, induces changes in HSC differentiation and gene expression that returned rapidly to normal but also establish novel open chromatin...
2h
Contributors : Shipra Vaishnava ; Namrata IyerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNAseq analysis of laser capture microdissected ileal epithelial cells from stopFlox(control) and stopdIEC (epithelium-specific vitamin A signaling knockdown) mice
2h
Contributors : Daan R van der Veen ; Emma E Laing ; Sung-Eun Bae ; Jonathan D Johnston ; Derk-Jan Dijk ; Simon N ArcherSeries Type : Expression profiling by arrayOrganism : Mus musculusPolymorphisms in human circadian clock gene PERIOD3 (PER3) are associated with a wide variety of phenotypes such as diurnal preference, delayed sleep phase disorder, sleep homeostasis, cognitive performance, bipolar disorder, type 2 diabetes, cardiac regulation, cancer, light sensitivity, hormone and cytokine secretion,...
2h
Contributors : Shin-ichi Oka ; Adave Chin ; Jiyeon Park ; Shohei Ikeda ; Wataru Mizushima ; Guersom Ralda ; Peiyong Zha ; Mingming Tong ; Jaemin Byun ; Fan Tang ; Yudai Einaga ; Chun-yang Huang ; Toshihide Kashihara ; Bin Tian ; Yoko Hirabayashi ; Junji Yodoi ; Junichi SadoshimaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate the role of Trx1 in the heart, cardiomyocyte-specific Trx1 knockout mice were generated. RNA-sequencing...
2h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Wenliang Wang ; Golnaz VahediSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensWe report the development of a novel method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the...
2h
Contributors : Wenliang Wang ; Golnaz VahediSeries Type : Other ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe report the development of a novel method called EpiVIA (https://github.com/VahediLab/epiVIA) for the joint profiling of the chromatin accessibility and lentiviral integration site analysis at the population and single-cell levels. We validate our technique in clonal cells with previously defined integration sites and further demonstrate the...
2h
Contributors : Yanqin Yang ; Jia Wang ; Lu Zhang ; Caifeng Sun ; Ying Wang ; Haoyu Dong ; Han Zhang ; Xingjie Gao ; Chuanzhou Gao ; Bin Zhang ; Bin Feng ; Weifeng MaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe cumulatively radiated a glioblastoma cell line, U87MG, and screened radioresistant glioma cells. A transcriptome sequencing was performed to analyze the transcription differences between the raidoresistant and control cells.
2h
Contributors : Marc K Halushka ; Suraj Kannan ; Brian L Lin ; Rohan VermaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBackground: Skeletal muscle myocytes have evolved into slow and fast-twitch types. These types are functionally distinct as a result of differential gene and protein expression. However, an understanding of the complexity of gene and protein variation between myofibers is unknown.Methods: We performed deep, whole cell, single cell RNA-seq...
2h
Contributors : James I Stewart ; Vinicius M Fava ; Joshua D Keraert ; Adithya S Subramanian ; Fabrice N Gravelat ; Melanie Lehoux ; P L Howell ; Robert A Cramer ; Donald C SheppardSeries Type : Expression profiling by high throughput sequencingOrganism : Aspergillus fumigatusInhalation of conidia of the opportunistic mold Aspergillus fumigatus by immunocompromised hosts can lead to invasive pulmonary disease. Inhaled conidia that escape immune defenses germinate to form filamentous hyphae that invade...
2h
Contributors : Jens Eberlein ; Dirk HomannSeries Type : Expression profiling by arrayOrganism : Mus musculusThe spectrum of pathogen-specific CD8+T cell functionalities, including their chemokine production profiles, remains incompletely defined. Here, we have employed microarray analyses to determine the gene expression profiles of lymphocytic choriomeningits virus- (LCMV-) specific effector (TE) and memory (TM) CD8+T cells in the established p14 chimera model; analyses of p14 TE and TM expression...
2h
Contributor : Zhihong LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Capra hircusOBJECTIVE: To study the function of DP cells during the development of hair follicles in cashmere goats, we used single-cell sequencing to perform transcriptome sequencing of skin samples from different periods.Method: Single cell barcoding and library preparation were performed based on 10x Genomics single-cell RNA sequencing platform, CellRanger (v2.2.0) software was used for analyzing...
2h
Contributors : Alaksh Choudhury ; Olivier Tenaillon ; Ryan T GillSeries Type : OtherOrganism : Escherichia coliDeep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single...
2h
Contributors : Ann M Kemper ; Jenny Drnevich ; Molly E McCue ; Annette M McCoySeries Type : Expression profiling by high throughput sequencingOrganism : Equus caballusWe report differential expression analysis of RNAseq data in joint-related tissues (articular cartilage and subchondral bone) in healthy foals (4 weeks of age or younger) and healthy adult horses. We find that 1115 genes are differentially expressed in cartilage and 3574 in bone between these two groups. Functional annotation suggests...
2h
Contributors : Amel Dudakovic ; HwaKyung Nam ; Andre van Wijnen ; Nan E HatchSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSeverity of craniosynostosis in humans varies widely even in patients with identical genetic mutations, and severity corresponds with morbidity. In this study we compared RNA sequencing data from cranial tissues of a severe form of Crouzon craniosynostosis syndrome (C57BL/6 FGFR2C342Y/+ mice) with those of a less severe form of Crouzon...
2h
Contributors : Aurore Sanchez ; Xiaojing Mu ; Valérie Borde ; Scott KeeneySeries Type : OtherOrganism : Saccharomyces cerevisiaeProgrammed DNA double-strand breaks (DSBs) initiate meiotic recombination and their subsequent repair culminates in crossover (CO) formation. COs result from the asymmetric cleavage of double-Holliday junction (dHJ) intermediates, that requires the MutLγ endonuclease and a non-catalytic function of Exo1, an activity essential for fertility but at risk of generating unwanted...
2h
Contributors : S Suthaporn ; K Jayaprakasan ; J G Thornton ; K F Walker ; J H Hernandez-Medrano ; M Castellanos ; S T May ; I Khanc ; W E MaaloufSeries Type : Expression profiling by arrayOrganism : Homo sapiensAbnormally low progesterone results in an aberrance of endometrial gene expression affecting the chance of implantation. Therefore, serum progesterone monitoring for embryo transfer in the natural cycle is useful and it seems to be potentially applicable for artificial cycles with using...
2h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Toxoplasma gondiiThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Yu Zheng ; Yong ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpers: To verify the effect of adjuvants (Alhydrogel, AS02, AS03) on immunity of BALB/c mice induced by RSV-F subunit vaccine at the level of gene expression. Methodes:Four groups ((1) RSV-F, (2) RSV-F + Alhydrogel, (3) RSV-F + AS02, and (4) RSV-F + AS03) were analyzed in the transcriptome sequencing experiment. On days 0 and 14, vaccines were administered intramuscularly...
2h
Contributors : Simona Seizova ; Chris J Tonkin ; Alexandra L GarnhamSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Toxoplasma gondiiThe purpose of these data is to determine if the impact bradyzoites have on the host transcripton is dependent on the export of parasite effector proteins via Myr1. We found that the expression of 3,068 host genes (~42%) were dependent on Myr1. A further 4,312 were altered in the same direction when comparing both the wild...
2h
Contributors : John E Carlson ; Wanyan Wang ; Lawrence B Smart ; Craig H CarlsonSeries Type : Expression profiling by high throughput sequencingOrganism : Salix x rubraShrub willow (Salix spp.), a short rotation woody biomass crop, has superior properties as a perennial energy crop for the Northeast and Midwest US. However, the insect pest potato leafhopper Empoasca fabae (Harris) (PLH) can cause serious damage and reduce yield of susceptible genotypes. Currently, the willow cultivars in use display...
2h
Contributors : Ramona Bledea ; Varshini Vasudevaraja ; Seema Patel ; James Stafford ; Jonathan Serrano ; Gianna Esposito ; Andreas Kloetgen ; John G Golfinos ; David Zagzag ; Britta Weigelt ; Snjezana Dogan ; Jorge S Reis-Filho ; Sarah Chiang ; Dimitris Placantonakis ; Aristotelis Tsirigos ; Matija SnuderlSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensBackground: IDH1/2 mutations are present in cancer arising from various tissues; however, common and...
2h
Contributors : Degui Geng ; Eduardo DavilaSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensGenome-wide DNA methylation analysis of over 850,000 methylation sites was performed using the Infinium MethylationEPIC BeadChip (Illumina) in RPMI7951, C32, Malme-3M, SK-MEL-28, EPZ-6438-treated C32, azacytidine-treated Malme-3M, and DMSO- or NU7441-treated Mb3429 cells.
2h
Contributors : Jo A Stratton ; Jason Plemel ; Jeff BiernaskieSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo isolate Cx3cr1 fate mapped cells following lysolecithin-induced demyelination in the spinal cord, we performed stereotaxic injection of lysolecithin into the ventral white matter tract of the thoracic spinal cord in adult Cx3cr1-CreER:Rosa26-tdTomato+ve mice treated with tamoxifen 4 weeks previously. We FACS collected viable tdTomato+ve cells from...
2h
Contributors : M G Roukens ; A R Lourenço ; P J CofferSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-sequencing of human mammary epithelial cells (HMLEs) that were lentivirally transduced with vector that constitutively expresses C/EBPα and its respective empty vector control. Both lines were analyzed with and without TGF-β treatment.
2h
Contributors : Jungwook Park ; Boknam Jung ; Jungkwan Lee ; Young-su SeoSeries Type : Expression profiling by high throughput sequencingOrganism : Fusarium graminearumBacterial pathogen Burkholderia glumae and fungal pathogen Fusarium graminearum cause similar disease symptoms and are often co-isolated from rice heads, inferring interactions between the two pathogens. F. graminearum is resistant to the bacterial toxin toxoflavin, a strong anti-microbial activity, produced by B. glumae. We isolated...
2h
Contributors : Yukihide Maeda ; Shin Kariya ; Junko Takahara ; Shohei Fujimoto ; Akiko Sugaya ; Kazunori NishizakiSeries Type : Expression profiling by arrayOrganism : Mus musculusIn order to elucidate molecular mechanisms of noise-induced hearing loss in the cochlea (inner ear), transcriptome of the cochlear sample was analyzed after induction of hearing loss by exposure to intense noise in mice. Cochlear transcriptome was analyzed at 3 hours following the noise exposure.
5h
Contributors : Benjamin D Weger ; Cedric Gobet ; Eva Martin ; Frederic Gachon ; Felix NaefSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAlmost all organisms on earth show daily rhythms of physiology. These rhythms are mainly generated mainly by the interaction between the circadian clock and feeding rhythms. Transcriptomics has been extensively studied in genetically deprived clock models but the contribution of the strongly altered feeding rhythms in...
6h
Contributors : Robert Sabatini ; Rudo Kieft ; Alexandre P Marand ; Jose D Moran ; Robert Bridger ; Lance Wells ; Robert J SchmitzSeries Type : Expression profiling by high throughput sequencingOrganism : Trypanosoma bruceiBase J is a modified DNA base that is enriched at RNA polymerase II termination sites and telomeres. We previously found that base J functions to prevent readthrough transcription within gene clusters in T. brucei. We now identify a complex in Leishmania and T. brucei composed...
8h
Contributors : Jamie Wangen ; Rachel GreenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating...
10h
Contributors : Ashley M Laughney ; Jing Hu ; Nathaniel R Campbell ; Samuel F Bakhoum ; Manu Setty ; Vincent-Philippe Lavallée ; Yubin Xie ; Ignas Masilonis ; Ambrose J Carr ; Viola Allaj ; Marissa Mattar ; Joao Xavier ; Linas Mazutis ; John T Poirier ; Charles M Rudin ; Dana Pe'er ; Joan MassaguéSeries Type : Expression profiling by high throughput sequencingOrganism : Transcriptionally profiling of single cells isolated from progressive stages of metastatic outbreak in a mouse model of...
10h
Contributors : Jamie Wangen ; Rachel GreenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating...
10h
Contributors : Jamie Wangen ; Rachel GreenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating...
10h
Contributor : Michael BlowerSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Xenopus laevisChanges in gene expression are required to orchestrate changes in cell state during development. Most cells change patterns of gene expression through transcriptional regulation. In contrast, oocytes are transcriptionally silent and use changes in mRNA poly-A tail length to control protein production. Recent technical advances have enabled genome-wide measurement of poly-A...
10h
Contributors : Cassadra M Leech ; Heather E Arsenault ; Jianhong Ou ; Haibo Liu ; Lihua J Zhu ; Jennifer A BenantiSeries Type : Expression profiling by high throughput sequencingOrganism : Gene expression was quantified in crz1 hog1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. We show that calcineurin-dependent downregulation...
10h
Contributors : Daniele Musiani ; Marica-Rosaria Ippolito ; Enrico Massignani ; Sri-Ganesh Jammula ; Tiziana BonaldiSeries Type : Expression profiling by high throughput sequencingOrganism : PRMT1 is the major Arginine methyltransferase in mammalian cells and its over-expression in human cancer has been linked to poor response to cancer therapy. Here, combining mass spectrometry-based global methyl-proteomics with genome-wide mRNA expression profiling, we identify PRMT1 and its associated Arginine...
10h
Contributors : Jamie Wangen ; Rachel GreenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating...
10h
Contributors : Jamie Wangen ; Rachel GreenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensStop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough events can be therapeutically desirable when a premature termination codon (PTC) is found in a critical gene. To study SCR in vivo in a genome-wide manner, we treated mammalian cells with aminoglycosides and performed ribosome profiling. We find that in addition to stimulating...
10h
Contributors : A M Laughney ; J Hu ; N R Campbell ; S F Bakhoum ; M Setty ; V P Lavallée ; Y Xie ; I Masilonis ; A J Carr ; V Allaj ; M Mattar ; J Xavier ; L Mazutis ; J T Poirier ; C M Rudin ; D Pe'er ; J MassaguéSeries Type : Expression profiling by high throughput sequencingOrganism : By transcriptionally profiling single cells from patients spanning different stages of lung adenocarcinoma progression, we provide evidence of epithelial regeneration in untreated primary tumours and a...
10h
Series Type : Expression profiling by high throughput sequencingOrganism : This SuperSeries is composed of the SubSeries listed below.
10h
Contributors : Cassadra M Leech ; Heather E Arsenault ; Jianhong Ou ; Haibo Liu ; Lihua J Zhu ; Jennifer A BenantiSeries Type : Expression profiling by high throughput sequencingOrganism : Gene expression was quantified in crz1 delete S. cerevisae cells over a time course following calcineurin activation by CaCl2. Cells were pretreated with buffer or the calcineurin inhibitor FK506 to allow the identification of calcineurin-regulated genes. A strain with a calcineurin-resistant mutation in the...
10h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
11h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
13h
Contributors : Brooke C Wilson ; Ambra Annibali ; Lena Boehme ; Alan Hodgkinson ; Thomas S Carroll ; Rebecca J Oakey ; Vlad C SeitanSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusZbtb11 is an uncharacterised transcription factor that is conserved in vertebrates. Mutations in its human gene cause a form of inherited intellectual disablity, while in zebrafish Zbtb11 mutations lead to impaired...
14h
Contributors : Min-Ae Song ; Daniel Y Weng ; Peter G ShieldsSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensE-cig use is continuing to increase, particularly among youth never-smokers, and is used by some smokers to quit. The acute and chronic toxicity of e-cig use is unclear generally in the context of increasing reports of inflammatory-type pneumonia in some e-cig users. To assess lung effects of e-cigs without nicotine or flavors, we conducted a pilot study with...
14h
Series Type : Expression profiling by array ; Methylation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
15h
Contributors : Annerieke Sierksma ; Ashley Lu ; Renzo Mancuso ; Nicola Fattorelli ; Nicola Thrupp ; Evgenia Salta ; Jesus Zoco ; David Blum ; Luc Buée ; Bart De Strooper ; Mark FiersSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPolygenic risk scores have identified that genetic variants without genome-wide significance still add to the genetic risk of developing Alzheimer’s disease (AD). Whether and how subthreshold risk loci translate into relevant...
15h
Contributors : Shafiq M Syed ; Pradeep S TanwarSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSummary: RNAseq analysis of Axin2+ and Axin2- endometrial epithelial cells shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- cells.Methods: Four-week-old Axin2rtTA; tetOH2BJGFP mice (n=3) were ovariectomized. After 2 weeks of rest, H2BJGFP was induced in Axin2+ cells by a single dose of doxycycline administered intraperitoneally and...
15h
Contributors : Katelynn Toomer ; Mengyao Yu ; Diana Fulmer ; Lilong Guo ; Neal Peterson ; Alex Drohan ; Breiona Catching ; Andy Wessels ; Joshua Lipschutz ; Francesca N Delling ; Xavier Jeunmaitre ; Christian Dina ; Ryan Collins ; Harrison Brand ; Mike Talkowski ; Rupak Mukherjee ; Simon Body ; Gary Hardiman ; Willian A da Silveira ; Starr Hazard ; Baolin Wang ; Maire Leyne ; Ronen Durst ; Roger Markwald ; Solena Le Scouranec ; Albert Hagege ; David Milan ; Jean-Jacques ...
15h
Contributors : Daniel Y Weng ; Min-Ae Song ; Peter G ShieldsSeries Type : Expression profiling by arrayOrganism : Homo sapiensE-cig use is continuing to increase, particularly among youth never-smokers, and is used by some smokers to quit. The acute and chronic toxicity of e-cig use is unclear generally in the context of increasing reports of inflammatory-type pneumonia in some e-cig users. To assess lung effects of e-cigs without nicotine or flavors, we conducted a pilot study with serial bronchoscopies...
15h
Contributors : Annerieke Sierksma ; Ashley Lu ; Renzo Mancuso ; Nicola Fattorelli ; Nicola Thrupp ; Evgenia Salta ; Jesus Zoco ; David Blum ; Luc Buée ; Bart De Strooper ; Mark FiersSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPolygenic risk scores have identified that genetic variants without genome-wide significance still add to the genetic risk of developing Alzheimer’s disease (AD). Whether and how subthreshold risk loci translate into relevant...
15h
Contributor : Ming HeSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensStrategies targeted vascular endothelial growth factor (VEGF)-dependent osteosarcoma progression are limited although important progress has been made in illustrating the mechanisms. Here we identified circ_001621 as one of the significantly upregulated circular RNAs (circRNAs) by circRNAs microarrays. We found that patients with high circ_001621 expression had a shorter survival time. Moreover, we found several...
16h
Contributors : Daniela A Grassi ; Per L Brattås ; Marie E Jönsson ; Ofelia Karlsson ; Diahann Atacho ; Sara Nolbrant ; Malin Parmar ; Johan JakobssonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) were differentiated into forebrain neural progenitors using a fully defined protocol with dual SMAD-inhibition. Cells were taken at four time points to monitor temporal changes in the...
16h
Contributors : Esther Tijchon ; Gouqiang Yi ; Amit Mandoli ; Jos Smits ; Francesco Ferrari ; Falco Wijnen ; Bowon Kim ; Eva M Janssen-Megens ; Jan J Schuringa ; Joost H MartensSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensHere we describe the development and characterization of an induced pluripotent stem cell (iPSC) system that allows in vitro differentiation towards different mature...
16h
Contributor : P BrestSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA homeostasis, a process maintained through a balance between transcription and decay, plays a critical role for most cellular functions. The conserved XRN and DIS3 families are major exoribucleases involved in this RNA turnover. Very little information is currently available about their physiological and physiopathological functions in humans. The aim of this study was to identify the...
16h
Contributors : Judith Lang ; Patrick Bohn ; Hilal Bhat ; Holger Jastrow ; Bernd Walkenfort ; Feyza Cansiz ; Julian Fink ; Michael Bauer ; Dominik Olszewski ; Ana Ramos-Nascimento ; Vikas Duhan ; Sarah-Kim Friedrich ; Katrin A Becker ; Adalbert Krawczyk ; Michael J Edwards ; Andreas Burchert ; Magdalena Huber ; Justa Friebus-Kardash ; Joachim R Göthert ; Cornelia Hardt ; Hans C Probst ; Fabian Schumacher ; Karl Köhrer ; Burkhard Kleuser ; Eduard B Babiychuk ; Beate Sodeik ; Jürgen...
16h
Contributors : Daniel A Lorenz ; Shashank Sathe ; Jacyln M Einstein ; Gene W YeoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe report the direct RNA sequencing of HEK293 and a primary human mammary epithelial cell (HMEC) line using Oxford Nanopore based sequencing. Using this data, we built an algorithm to detect m6A modifications within the DRACH motif context. Evaluation of m6A sites was carried out with HEK METTL3 knockdown and HMEC ALKBH5 over expression...
16h
Contributors : Dominika Foretek ; Marina Pinskaya ; Marc Gabriel ; Antonin MorillonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensXrn1 is a cytoplasmic 5’-3’ exoribonuclease responsible for degradation of multiple types of RNA. Data obtained on yeast model described Xrn1 function in degradation of messenger (m)RNA, Rapid transfer (t)RNA Decay (RTD) of hypomodified and unstable tRNA transcripts as well as maturation of 25S ribosomal (r)RNA and small nucleolar...
16h
GSE69901 Gene Expression Profiling Of Spinal Cord Injured Patients With Intractable Neuropathic Pain
Contributors : Bilge Yılmaz ; Emre AdıgüzelSeries Type : Expression profiling by arrayOrganism : Homo sapiensObjective: Chronic pain is a major problem in patients with spinal cord injury (SCI). According to different studies, approximately 70% of patients with SCI experience persistent pain. Although previous gene expression profiling studies have been conducted in animal models, gene expression profiling study in human whole blood has not been reported yet. The objective of this study was to...
17h
Contributors : Aniruddha Chatterjee ; Sarah Bowden ; Peter Stockwell ; Euan Rodger ; Michael Eccles ; Cherie StaynerSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensWe have previously described global hypomethylation and site-specific DNA methylation changes which are associated with disease-state renal tissue in Autosomal Dominant Polycystic Kidney Disease (ADPKD). However, to-date there are no available data on the pattern of DNA methylation across an...
17h
Contributors : Liwen Zhang ; Weiming WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDiabetic nephropathy (DN) is characterized by metabolic disorder and inflammation. However, the regulatory effects that long noncoding RNAs (lncRNAs) have on the pathogenesis of DN and on the efficacy of rosiglitazone treatment has yet to be clearly defined. Herein, we performed unbiased RNA sequencing to characterize the transcriptomic profiles in db/db diabetic mouse...
17h
Contributors : Julian Broche ; Daniel Hofacker ; Laura Laistner ; Sabrina Adam ; Pavel Bashtrykov ; Albert JeltschSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensEpigenome editing is a promising technology, potentially allowing the stable reprogramming of gene expression profiles without alteration of the DNA sequence. Targeted DNA methylation has been successfully documented by many groups for silencing of selected genes, but recent publications have...
22h
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