Contributors : Momoko Takagi ; Fuminori Takahashi ; Kazuya IchimuraSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaTo compare expression of defense-related genes between WT and smn2 mutant, we performed the RNA-seq analysis using the total RNA prepared from Arabidopsis WT and smn2 seedlings. RNA-seq profiling showed 250 Differentially Expressed Genes (DEGs) detected in smn2 compared to WT. Genome-wide mapping of DEG regions was also performed to elucidate...
2h
Contributors : Dan Naylor ; Ryan McClueSeries Type : Expression profiling by high throughput sequencingOrganism : soil metagenomePurpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia.Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either...
2h
Contributors : Jenny Joutsen ; Alejandro J Da Silva ; Jens C Luoto ; Marek A Budzynski ; Anna S Nylund ; Aurelie de Thonel ; Jean-Paul Concordet ; Valérie Mezger ; Délara Sabéran-Djoneidi ; Eva Henriksson ; Lea SistonenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA sequencing (RNA-seq) was used to study the impact of heat shock factors 1 and 2 (HSF1 and HSF2) on gene expression in normal growth conditions, upon Bortezomib-induced proteasome inhibition...
2h
Contributors : Elisa Laurenti ; Hugo P Bastos ; Nicole Mende ; Kourosh Saeb-Parsy ; Krishnaa Mahbubani ; Abbie CurdSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHaematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), the precursors of all blood cells, reside predominantly in the bone marrow (BM). Recent evidence suggests that other anatomical sites may contribute significantly to blood production, but the cellular, molecular and functional...
2h
Contributors : Yanjun Li ; Huili Hu ; Yaoqin GongSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensGiven that colorectal cancer stem cells (CCSCs) play key roles in the tumor dormancy, metastasis and relapse, targeting CCSCs is a promising strategy in cancer therapy. Here, we aimed to identify new regulators of CCSCs and found that Cullin 4B (CUL4B), which possesses oncogenic properties in multiple solid...
2h
Series Type : Genome variation profiling by genome tiling array ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Ana T Vidakovic ; Richard Mitter ; Jesper Q SvejstrupSeries Type : OtherOrganism : Homo sapiensIn response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNAPII and genome-wide transcription shutdown. How these responses are connected has remained unclear. Here we show that damage-induced ubiquitylation of RNAPII itself, at a single lysine (RPB1 K1268), is the focal point for DNA damage...
2h
Contributors : Elizabeth Lenkiewicz ; Smriti Malasi ; Martin Fernandez-Zapico ; Derek Cridebring ; Tara L Hogenson ; Mitesh J Borad ; Kendall Chambers ; Nirakar Rajbhandari ; Tannishtha Reya ; Yuning Xiong ; Jeong-Heon Lee ; Zhenqing Ye ; Huihuang Yan ; Tamas Ordog ; Matthew Hernandez ; Jennifer L Leiting ; Mark J Truty ; Daniel D Von Hoff ; Michael T BarrettSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe applied DNA content flow...
2h
Contributors : Ana Tufegdzic Vidakovic ; Richard Mitter ; Jesper Q SvejstrupSeries Type : OtherOrganism : Homo sapiensIn response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNAPII and genome-wide transcription shutdown. How these responses are connected has remained unclear. Here we show that damage-induced ubiquitylation of RNAPII itself, at a single lysine (RPB1 K1268), is the focal point for...
2h
Contributors : Shuichi Fujiwara ; Teruya Kawamoto ; Yohei Kawakami ; Yasufumi Koterazawa ; Hitomi Hara ; Toshiyuki Takemori ; Kazumichi Kitayama ; Shunsuke Yahiro ; Tomoyuki Matsumoto ; Takehiko Matsushita ; Takahiro Niikura ; Michiyo Koyanagi ; Toshihiro Akisue ; Takashi Aoi ; Ryosuke KurodaSeries Type : Expression profiling by arrayOrganism : Homo sapiensCancer stem cells (CSCs) are proposed to be unique subsets of clones within a tumor, attributed with tumor progression, resistance...
2h
Contributors : Yuliang Wang ; Hannele Ruohola-BakerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRegulation of embryonic diapause, dormancy that interrupts the tight connection between develop- mental stage and time, is still poorly understood. Here, we characterize the transcriptional and metabolite profiles of mouse diapause embryos and identify unique gene expression and metabolic signatures with activated lipolysis, glycolysis, and metabolic pathways...
2h
Contributors : William Nauseef ; Christine Cho ; Ryan McClure ; Caroline Genco ; Michael ApicellaSeries Type : Expression profiling by high throughput sequencingOrganism : Neisseria gonorrhoeae 1291These experiments examined the transcriptomic response of N. gonorrhoeae 1291 to incubation with human PMNs under three different timepoints, 10 minutes, 180 minutes and 360 minutes.
2h
Contributors : Sylvia E Fischer ; Gary RuvkunSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Caenorhabditis elegansTo examine the roles of the ADAR genes and the ERI-6/7 helicase in endogenous RNAi pathways, we sequenced small RNA of adr-1; adr-2; eri-6 mutants. We also analyzed the transcriptomes of these mutants using total RNAseq and mRNAseq. mRNAseq was done in mutants depleted for the RNAi factors drh-1 and...
2h
Contributors : Jason K Sicklick ; Hyunho YoonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo identify mRNA profiles in GIST and CAFs, we performed RNA sequencing analysis (RNA-seq) using GIST cell lines, GIST-T1 and GIST882, and CAFs.
2h
Contributors : Christoph Owenier ; Julia Hesse ; Christina Alter ; Zhaoping Ding ; Aseel Marzoq ; Patrick Petzsch ; Karl Köhrer ; Jürgen SchraderSeries Type : Expression profiling by arrayOrganism : Mus musculusMyocardial infarction (MI) leads to activation of cardiac fibroblasts (aCFs) and at the same time induces the formation of epicardium-derived cells at the heart surface. To discriminate between the two cell populations, we elaborated a fast and efficient protocol for the simultaneous...
2h
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
2h
Contributor : Sara WickströmSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensRNA and H3K9me3 ChIP sequencing data of normal human neonatal keratinocytes subjected to 40% uniaxial cyclic stretch
2h
Contributors : Ana T Vidakovic ; Richard Mitter ; Jesper Q SvejstrupSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, involving transcription-coupled DNA repair, degradation of RNAPII and genome-wide transcription shutdown. How these responses are connected has remained unclear. Here we show that damage-induced ubiquitylation of RNAPII itself, at a single lysine...
2h
Contributors : Seulgi Jung ; Wenting Liu ; Jiwon Baek ; Jung Moon ; Byong Ye ; Ho-Su Lee ; Sang Park ; Suk-Kyun Yang ; Buhm Han ; Jianjun Liu ; Kyuyoung SongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed RNA sequencing to produce expression quantitative trait loci (eQTL) database of Crohn's disease patients. Using this eQTL data, we tried to determine the most functionally relevant genes at the established Crohn’s disease loci identified...
2h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
2h
Contributors : Yibo Geng ; Liwei ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensProtein Tyrosine Phosphatase Receptor Type N (PTPRN) plays an important role in diabetes and many cancers but its role in glioma remain poorly defined. Here, we firstly verified PTPRN expression was negatively correlated with overall survival of glioblastoma patients. Moreover, suppression of PTPRN expression reduced both U87 and U343 cell viability, suppressed proliferation,...
2h
Contributors : Francisco J Aulestia ; Johnny Groeling ; Guilherme H Bomfim ; Veronica Costiniti ; Vinu Manikandan ; Ariya Chaloemtoem ; Axel R Concepcion ; Yi Li ; Larry E Wagner II ; Youssef Idaghdour ; David I Yule ; Rodrigo S LacruzSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe analyzed the effects of fluoride exposure in mouse enamel cells to assess its impact on cell Ca2+ signaling
2h
Series Type : Expression profiling by high throughput sequencingOrganism : Bos taurusObjectives: Identify gene products that characterize the biological status of typical calves which have been recently weaned, transported, and co-mingled prior to arrival at stocker facilities in order to identify gene products associated with BRD resistance.Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina HiSeq 3000. Individual samples were processed using an adaptation of the...
2h
Contributors : Francisco J Aulestia ; Johnny Groeling ; Guilherme H Bomfim ; Veronica Costiniti ; Vinu Manikandan ; Ariya Chaloemtoem ; Axel R Concepcion ; Yi Li ; Larry E Wagner II ; Youssef Idaghdour ; David I Yule ; Rodrigo S LacruzSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe analyzed the effects of fluoride exposure in mouse enamel cells to assess its impact on cell Ca2+ signaling
2h
Contributors : Kai Song ; Runwei Zhang ; Chunxiao ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Epinephelus coioidesIn order to obtain complete transcriptome data of epinephelus coioides
2h
Contributors : Chichao Chen ; Scott LoweSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusTo study transcriptomic changes upon PDXK knock-out in mouse and human leukemic cells
3h
Contributors : Bo Li ; Lingbo Zhang ; ChiChao Chen ; Scott LoweSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo validate the transcriptome profiling changes upon pharmacologic inhibition of PDXK, a key enzyme in vitamin B6 metabolism pathway, mouse leukemic cells were treated with PDXK inhibitor OMP. mRNA was extracted and purified for RNA_seq.
3h
Contributors : Aseda Tena ; Frederick W AltSeries Type : Other ; Expression profiling by high throughput sequencingOrganism : Mus musculusOur laboratory identified robust recurrent DNA double-strand break (DSB) cluster (“RDC”) genes in mouse neural stem/progenitor cells (NSPCs) by applying the high-throughput, genome-wide, translocation sequencing (HTGTS) method. Genomic alterations of most of the identified RDC-genes have been associated with psychiatric disorders such as autism and schizophrenia...
4h
Contributors : Aseda Tena ; Yuxiang Zhang ; Nia Kyritis ; Anne Devorak ; Jeffrey Zurita ; Pei-Chi Wei ; Frederick W AltSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusOur laboratory identified robust recurrent DNA double-strand break (DSB) cluster (“RDC”) genes in mouse neural stem/progenitor cells (NSPCs) by applying the high-throughput, genome-wide, translocation sequencing (HTGTS) method. Genomic alterations of most of the identified RDC-genes...
4h
Contributors : Janaki M Vinnakota ; Robert Zeiser ; Geoffroy Andrieux ; Melanie BoerriesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusUnderstanding the role of myeloid cells in GvHD of CNS. Microglia are the major immune cells of the CNS. We intend to understand if microglia play a role in GvHD of the CNS.
4h
Contributors : L Enz ; T Zeis ; F Geier ; D Schmid ; G Steiner ; U Certa ; N Schaeren-WiemersSeries Type : Expression profiling by arrayOrganism : Homo sapiensMultiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the brain. Among characteristics of MS pathology are cortical grey matter abnormalities, which have been linked to clinical signs such as cognitive impairment. To understand MS cortical grey matter pathogenesis, we performed differential gene expression analysis...
4h
Contributors : L Enz ; T Zeis ; F Geier ; D Schmid ; G Steiner ; U Certa ; N Schaeren-WiemersSeries Type : Expression profiling by arrayOrganism : Homo sapiensMultiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the brain. Among characteristics of MS pathology are cortical grey matter abnormalities, which have been linked to clinical signs such as cognitive impairment. To understand MS cortical grey matter lesion pathogenesis, we performed differential gene expression...
4h
Contributors : Doug Hanniford ; Andreas Kloetgen ; Eva HernandoSeries Type : OtherOrganism : Homo sapiensMetastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover important tumor biology and/or yield promising therapeutic insights. Here we investigated the role of circular RNAs (circRNA) in metastasis, using melanoma as a model aggressive tumor. We identified silencing of Cerebellar Degeneration Related 1 (CDR1as), a regulator of...
4h
Contributors : Doug Hanniford ; Andreas Kloetgen ; Eva HernandoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMetastasis is the primary cause of death of cancer patients. Dissecting mechanisms governing metastatic spread may uncover important tumor biology and/or yield promising therapeutic insights. Here we investigated the role of circular RNAs (circRNA) in metastasis, using melanoma as a model aggressive tumor. We identified silencing of Cerebellar Degeneration...
4h
Contributors : Tsudoi Toyoda ; Kota Iida ; Tomoko Ishijima ; Keiko Abe ; Shinji Okada ; Yuji NakaiSeries Type : Expression profiling by arrayOrganism : Mus musculusA recent study showed that 54% of type 2 diabetes (T2D) patients have nonalcoholic fatty liver disease, which is a risk factor for aggravation diabetic symptoms. Previous studies suggested components in maple syrup alleviated liver injury and found polyphenols as food components to improve the symptoms and complications of diabetes....
5h
Contributors : Yang Yu ; Eric LaiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusNeural development is tightly controlled at multiple levels to orchestrate appropriate choices of cell fate and differentiation. While more attention has been paid to the roles of neural-restricted factors, broadly-expressed factors can have compelling impacts on tissue-specific development. Here, we describe in vivo genetic analysis of Ars2, which has mostly been...
5h
Contributors : Robert A Policastro ; Gabriel E ZentnerSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Saccharomyces cerevisiaeAccurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid,...
9h
Contributors : Kari J Kurppa ; Pasi A JänneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEradicating tumor dormancy that develops following oncogene-targeted therapy, including after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer (NSCLC), is an attractive therapeutic strategy but the mechanisms governing the establishment of tumor dormancy are poorly understood. We observe that blockade...
10h
Contributors : Kari J Kurppa ; Pasi A JänneSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensEradicating tumor dormancy that develops following oncogene-targeted therapy, including after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer (NSCLC), is an attractive therapeutic strategy but the mechanisms governing the establishment of tumor dormancy are poorly understood. We observe...
10h
Contributors : Kari J Kurppa ; Pasi A JänneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEradicating tumor dormancy that develops following oncogene-targeted therapy, including after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer (NSCLC), is an attractive therapeutic strategy but the mechanisms governing the establishment of tumor dormancy are poorly understood. We observe that blockade...
10h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
10h
Contributors : Kari J Kurppa ; Pasi A JänneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEradicating tumor dormancy that develops following oncogene-targeted therapy, including after epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) treatment of EGFR-mutant non-small cell lung cancer (NSCLC), is an attractive therapeutic strategy but the mechanisms governing the establishment of tumor dormancy are poorly understood. We observe that blockade...
10h
Contributor : Nancy L GuoSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusPrinter emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA)...
11h
Series Type : Expression profiling by arrayOrganism : Rattus norvegicus ; synthetic constructThis SuperSeries is composed of the SubSeries listed below.
11h
Contributor : Nancy L GuoSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusPrinter emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA)...
11h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
11h
Contributor : Nancy L GuoSeries Type : Expression profiling by arrayOrganism : Rattus norvegicus ; synthetic constructPrinter emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency...
11h
Contributor : Nancy L GuoSeries Type : Expression profiling by arrayOrganism : Rattus norvegicus ; synthetic constructPrinter emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency...
11h
Contributors : Thibault Godard ; Daniela Zühlke ; Georg Richter ; Melanie Wall ; Katharina Riedel ; Manfred Rohde ; Ignacio Poblete-Castro ; Rainer Krull ; Rebekka BiedendieckSeries Type : Expression profiling by arrayOrganism : Bacillus megaterium DSM 319First transcriptome analyses of Bacillus megaterium DSM319 grown under mild and severe salt stress (up to 1.8 M NaCl) to analyse the addaptation of the organism on transcriptome level
11h
Contributors : Alexander Y Nikitin ; Dah-Jiun FuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe report the gene expression profiles of gastric squamous-columnar junction cancer derived from the mice with conditionally inactivation of Trp53 and Rb1 genes in Lgr5+ cells
11h
Contributors : Wen Xiao ; Xiaoping ZhangSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensMicroRNAs (miRNAs) expression profiles are widely investigated in the major cancers, but their expression in patients plasmas of cancers have not yet to be fully elucidated. We investigated expression profiles of miRNAs in patients preoperative/postoperative plasmas of clear cell renal cell carcinomas (ccRCCs) by using a miRNAs microarray platform which covers a total of 1,523 human miRNAs.
12h
Contributors : Jingtao Guo ; Bradley CairnsSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe human testis undergoes dramatic developmental and structural changes during puberty, including proliferation and maturation of niche/somatic cells, and the onset of spermatogenesis. Here, we profiled and analyzed single-cell transcriptomes of ~10,000 testicular cells from four boys spanning puberty, and compared to infants and adults. During puberty, undifferentiated...
12h
Contributors : Johanna Kurko ; Craig R PrimmerSeries Type : Expression profiling by arrayOrganism : Salmo salarStudy revealed new information about molecular functions of the vgll3, akap11 and six6 genes associated with age-at-maturity in Atlantic salmon
12h
Contributors : Paolo Casali ; Hong Zan ; Yidong Chen ; Tabrez A MohammadSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensShort-chain fatty acids (SCFAs) butyrate and propionate are metabolites from dietary fibers fermentation by gut microbiota that can affect differentiation or functions of T cells, macrophages and dendritic cells. We show here that these SCFAs directly impact B cells to modulate in...
12h
Contributors : Yuan Tian ; Grégory Seumois ; Sara Herrera de la Mata ; Pandurangan Vijayanand ; Bjoern Peters ; Daniela Weiskopf ; Alessandro SetteSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDengue virus (DENV) infection is associated with a range of clinical manifestations, from self-limiting dengue fever (DF) to life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Although DENV-specific CD4 T cells are capable of producing...
12h
Contributors : Qiang Feng ; Wenyan KangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo better understand the global responses of GMSCs to F. nucleatum infection along the time sequence, we performed a genome-wide transcriptome analysis by RNA-sequencing technology to determine the global changes on gene expression level
13h
Contributors : Marco Bizzarri ; Massimo Delledonne ; Alberto Ferrarini ; Paola Tononi ; Elisa Zago ; Doriano Vittori ; Francesco Damiani ; Francesco PaolocciSeries Type : Expression profiling by arrayOrganism : Helianthus tuberosusHelianthus tuberosus L., known as the Jerusalem Artichoke, is a hexaploid plant species, adapted to low nutrient soils, that accumulates high levels of inulin in its tubers. Inulin is a fructose-based polysaccharide used either as dietary fiber or for the production...
13h
Contributors : Naofumi Asano ; Hideyuki Takeshima ; Satoshi Yamashita ; Eisuke Kobayashi ; Akira Kawai ; Tadashi Kondo ; Toshikazu UshijimaSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensDNA methylation in osteosarcoma and Ewing sarcoma
13h
Contributors : Michael Black ; Rance NaultSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusAcetamide (CAS 60-35-5) is detected in common foods including milk, eggs, beef, and roasted coffee beans. Chronic rodent bioassays using high doses (≥1000 mg/kg/day) suggest acetamide is a group 2B possible human carcinogen due to the induction of liver tumors. Weight-of-evidence indicates acetamide is not genotoxic, and therefore a threshold response is expected....
13h
Contributors : Yuichi Mitobe ; Kaori Iino ; Kazuhiro Ikeda ; Kuniko Horie-Inoue ; Satoshi InoueSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo examine the role of PSF and NONO in estrogen-dependent breast cancer, MCF-7 cells were treated with siRNA targeting PSF, NONO or control siRNA (siControl). Microarray analysis revealed PSF- or NONO-regulated genes in MCF-7 cells.
13h
Contributors : Yuichi Mitobe ; Kaori Iino ; Kazuhiro Ikeda ; Kuniko Horie-Inoue ; Satoshi InoueSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo examine the role of NONO in estrogen-independent breast cancer, MDA-MB-2317 cells were treated with siRNA targeting NONO or control siRNA (siControl). Microarray analysis revealed NONO-regulated genes in MDA-MB-231 cells.
13h
Contributors : Ginevra Brocca ; Massimo CastagnaroSeries Type : Genome variation profiling by genome tiling arrayOrganism : Canis lupus familiarisThe aim of this work was to identify the Copy Number Aberrations (CNAs) by high-resolution array Comparative Genomic Hybridization (aCGH) on 19 formalin-fixed, paraffin-embedded (FFPE) samples of treatment-naïve COM.
13h
Contributors : Shuai Zhao ; Ting ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Talaromyces pinophilusTranscriptomic profiling and real-time quantitative reverse transcription-PCR analyses revealed that TP05746 dynamically regulated the expression of genes encoding major PBDEs. Furthermore, in vitro binding experiments confirmed that TP05746 directly bound to the promoter regions of these major enzyme genes.Transcription factors mediated the regulation of plant-biomass-degrading...
13h
Contributors : Danielle L Rudler ; Laetitia Hughes ; Kara L Perks ; Tara Richman ; Irina Kuznetsova ; Judith A Ermer ; Laila N Abudulai ; Anne-Marie J Shearwood ; Helena M Viola ; Livia C Hool ; Stefan J Siira ; Oliver Rackham ; Aleksandra FilipovskaSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Mus musculusMammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs. To date it is not clear how mitoribosomes recognize...
13h
Contributors : Tiffany R Frey ; Jozan Brathwaite ; Brian Magnuson ; Saurabh Agarwal ; Mats Ljungman ; Michael T McIntosh ; Sumita Bhaduri-McIntoshSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensLytic activation from latency is a key transition point in the life cycle of herpesviruses. Epstein-Barr virus (EBV) is a human herpesvirus that can cause lymphomas, epithelial cancers, and other diseases, most of which require the lytic cycle. While the...
13h
Contributors : Brittney Lozzi ; Benjamin DeneenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goals of this study are to profile the molecular signatures of astrocytes from four brain regions (olfactory bulb, hippocampus, cortex, and brainstem) and determine if differential transcription factor enrichment may play a role in shaping astrocyte spatial diversity. We performed RNA-seq on astrocytes from the olfactory bulb, hippocampus, cortex, and brainstem,...
15h
Contributors : Zijie Zhang ; Agnieszka Chryplewicz ; Mark Eckert ; Chuan HeSeries Type : OtherOrganism : Homo sapiensWe developed RADAR , a method for detecting differential methylated loci in MeRIP-seq data. RADAR uses a flexible model to accommodate increased noise due to RNA immunoprecipitation and are compatible with complex study design. RADAR enabled accurate identification of altered methylation sites in patient samples where covariates need to be accounted for. We use the m6A-profiling...
15h
Contributors : Aditya Mithal ; Jed Mahoney ; Gustavo MostoslavskySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEfficient generation of human induced pluripotent stem cell (hiPSC)-derived human intestinal organoids (HIOs) would facilitate the development of in vitro models for a variety of diseases that affect the gastrointestinal tract, such as inflammatory bowel disease or Cystic Fibrosis.
15h
Contributors : Carlos Villacorta Martin ; Aditya Mithal ; Gustavo MostoslavskySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLung and hindgut directed differentiations with multiple protocols and time points
15h
Contributors : Yaqing Zhang ; Veerin Sirihorachai ; Katelyn DonahueSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn human patients and in mouse models, immunosuppressive regulatory T cells(Tregs)accumulate in Pancreatic Intraepithelial Neoplasia (PanIN), the precursor lesions to pancreatic cancer. Tregs are considered a potential therapeutic target with the goal to reverse immunosuppression in a number of malignancies, including pancreatic cancer. Here,...
16h
Contributor : Ma HailongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensInterferon-alpha (IFNα) plays a ciritical role in immune regulation, especially in tumor microenvironment. Our previous study has demonstrated that IFNα promoted immunosuppression formation in head and neck squamous cell carcinoma. To explore the mechanism underlying IFNα-induced immunosuppression, long noncoding RNA (lncRNA) sequece was conduted. We identified a novel IFNα-induced upregulated...
16h
Contributors : Flora Paldi ; Adele L MarstonSeries Type : OtherOrganism : Saccharomyces cerevisiaeHigh-resolution Hi-C in metaphase in wild type cells with and without tension, chl4Δ with tension, and sgo1-3A and sgo1Δ without tension
18h
Contributors : Bonnie Alver ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeGenome binding/occupancy profiling of Sgo1 by high throughput sequencing
18h
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencing ; OtherOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeThis SuperSeries is composed of the SubSeries listed below.
18h
Contributors : Bonnie Alver ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeGenome binding/occupancy profiling of the cohesin subunit Scc1 by high throughput sequencing
18h
Contributors : Bonnie Alver ; Adele L MarstonSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaePurpose: Are convergent genes at boundaries expressed?
18h
Contributors : Flora Paldi ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeGenome binding/occupancy profiling of the cohesin subunit Scc1 by high throughput sequencing. S. pombe is included as the calibration genome.
18h
Contributors : Bonnie Alver ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaePurpose: The goal is to determine the requirement for Chl4 in association of cohesin with the centromere and pericentromere boundaries
18h
Contributors : Flora Paldi ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeGenome binding/occupancy profiling of Sgo1 and the condensin subunit Brn1 by high throughput sequencing. S. pombe is included as the calibration genome.
18h
Contributors : Flora Paldi ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeGenome binding/occupancy profiling of Sgo1 and the condensin subunit Brn1 by high throughput sequencing. S. pombe is included as the calibration genome.
18h
Contributors : Flora Paldi ; Adele L MarstonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombeGenome binding/occupancy profiling of the cohesin subunit Scc1 by high throughput sequencing. S. pombe is included as the calibration genome.
18h
Contributors : Jose Hermida ; Mikel Allende ; Elizabeth Guruceaga ; Eva Molina ; Ramón Lecumberri ; Julen OyarzabalSeries Type : Expression profiling by arrayOrganism : Mus musculusBACKGROUNDAntithrombotic medications target coagulation factors. Their use is associated with an increased bleeding risk. Safer drugs are needed. We described that the heat shock protein 70 (Hsp70) exhibits antithrombotic properties that do not influence bleeding.OBJECTIVESBy using murine models, we want to test...
18h
Contributors : Alex Schulz ; Marco GrothSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe aimed at identifying a common transcriptional response of neurons to acute injury by conducting a RNA-Seq analysis on primary mouse neurons. We performed parallel damaging of cultured neurons by applying oxygen-glucose deprivation (OGD) as model for cerebral ischemia as well as excitotoxicity induced by the glutamate receptor agonist kainic acid (KA) as an in vitro model...
18h
Contributors : Chiara Stüdle ; Paola Occhetta ; Florian Geier ; Arne Mehrkens ; Andrea Barbero ; Ivan MartinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman bone marrow derived mesenchymal stromal cells (BMSCs) represent a putative cell source candidate for tissue engineering based strategies to repair cartilage and bone. However, traditional isolation of BMSCs by their preference to adhere to plastic leads to very heterogeneous cell populations and...
19h
Contributors : Urs Fisch ; Florian Geier ; Raphael GuzmanSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusPurpose: Recent findings indicate a regulatory role of microglia on neurogenesis in the SVZ in health and disease. Microglia in the early postnatal SVZ are not fully maturated and may react differently than adult microglia to injury. We sought to investigate the impact of cortico-striatal neonatal HI injury on the microglial phenotype in the early postnatal SVZ. Results:...
19h
Series Type : Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
19h
Contributors : Penny J Norsworthy ; Andrew G Thompson ; Tze H Mok ; Ross W Paterson ; Jonathan M Schott ; John Collinge ; Simon Mead ; Emmanuelle A ViréSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensSporadic Creutzfeldt-Jakob disease (sCJD) presents as a rapidly progressive dementia which is usually fatal within six months. No blood tests are currently available for diagnosis or disease monitoring. Here, we profile blood microRNA (miRNA) expression in...
22h
Contributors : Carlos Bas-Orth ; Hilmar BadingSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculusThe cellular consequences of N-Methyl-D-Aspartate receptor (NMDAR) stimulation depend on the receptors’ subcellular localization. Synaptic NMDARs promote plasticity and survival whereas extrasynaptic NMDARs mediate excitotoxicity and contribute to cell death in neurodegenerative diseases. The mechanisms that couple activation of extrasynaptic NMDARs to cell death remain incompletely...
22h
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