Series Type : Expression profiling by array
Organism : Homo sapiens
Endothelial cells play an important role in maintenance of the vascular system and the repair after injury. Under pro-inflammatory conditions, endothelial cells can acquire a mesenchymal phenotype by a process named endothelial-to-mesenchymal transition (EndMT), which affects the functional properties of endothelial cells. Here, we investigated the epigenetic control of EndMT. We show that the histone demethylase JMJD2B is induced by EndMT promoting pro-inflammatory and hypoxic conditions. Silencing of JMJD2B reduced TGF-β2-induced expression of mesenchymal genes and prevented the alterations in endothelial morphology and impaired endothelial barrier function. Endothelial-specific deletion of JMJD2B in vivo confirmed a reduction of EndMT after myocardial infarction. EndMT did not affect global H3K9me3 levels but induced a site-specific reduction of repressive H3K9me3 marks at promoters of mesenchymal genes, such as Calponin (CNN1), and genes involved in TGF-β signaling, such as AKT Serine/Threonine Kinase 3 (AKT3) and sulfatase 1 (SULF1). Silencing of JMJD2B prevented the EndMT-induced reduction of H3K9me3 marks at these promotors and further repressed these EndMT-related genes. Our study reveals that endothelial identity and function is critically controlled by the histone demethylase JMJD2B, which is induced by EndMT-promoting pro-inflammatory and hypoxic conditions and support the acquirement of a mesenchymal phenotype.
Contributors : Paul Brighton ; Maruyama Yojiro ; Katherine Fishwick ; Pavle Vrljicak ; Shreeya Tewary ; Risa Fujihara ; Joanne Muter ; Emma S Lucas ; Taihei Yamada ; Andrew Sharkey ; Laura Woods ; Raffaella Lucciola ; Saturo Takeda ; Sascha Ott ; Myriam Hemberger ; Siobhan Quenby ; Jan J BrosensSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe use RNA-sequencing to measure global transcription in LH timed endometrial biopsies of 10 women aged...
1h
Contributors : Angela Zhang ; Cindy Y Li ; Edward J Kelly ; Lianne Sheppard ; Julia Y CuiSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensPurpose: The goal of this study was to investigate how PBDEs regulate both PCGs and lncRNAs in a PXR/CAR ligand-dependent and independent mannerMethods: HepaRG cells, which are human-derived hepatic cells that accurately represent gene expression profiles of human liver tissue, were exposed to BDE-47 and BDE-99 at a...
1h
Contributors : Blanca Diaz-Castro ; Mohitkumar Gangwani ; Giovanni Coppola ; Baljit S KhakhSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe Khakh laboratory used gfaABC1D-RiboTag AAVs to purify and sequence astrocyte actively translated mRNAs from Huntington's disease mouse models at several stages of the disease. Two weeks after AAV injection, striata were homogenized and RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific...
1h
Contributors : Shahnaz Perveen ; Xinguang ZhuSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativaImprovement in the photosynthetic efficiency is a major approach to improve crop yield potential. So far, most of the demonstrated cases of photosynthesis improvement was achieved through manipulation of one or a few photosynthesis related genes. Present study found that over-expression of one maize transcription factor, mEmBP-1 gene, led to simultaneously increased...
1h
Contributors : Chitra Rawat ; Rintu Kutum ; Samiksha Kukal ; Ankit Srivastava ; Ujjwal R Dahiya ; Suman Kushwaha ; Sangeeta Sharma ; Debasis Dash ; Luciano Saso ; Achal K Srivastava ; Ritushree KukretiSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe aim here was to identify mRNA expression biomarkers associated with the disease epilepsy and the antiepileptic drug response. Gene expression profiles of drug-naïve patients with epilepsy were compared with that of healthy...
1h
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 variation profiling by genome tiling arrayOrganism : Homo sapiensWe applied DNA content flow cytometry to...
1h
Contributors : Jeremy W Roy ; Catherine A Taylor ; Annie-Pier Beauregard ; Daniel C Ayre ; Sheena Fry ; Simi Chacko ; Gabriel Wajnberg ; Andrew P Joy ; Ngoc-Neu Mai-Thi ; Nicolas Crapoulet ; David A Barnett ; Anirban Ghosh ; Stephen M Lewis ; Rodney J OuelletteSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensWe demonstrate a method for the DNA, RNA and Protein extraction of plasma extracellular vesicles.
1h
Contributors : Sarah A Justice ; Guihong Qi ; HR S Wijeratne ; Jose F Victorino ; Ed R Simpson ; Aruna B Wijeratne ; Amber L MosleySeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeRNA-seq experiments measuring global RNA abundanceTemperature sensitive (TS) mutants are a tool that have been foundational for the study of many essential life processes. Despite the long-term use of TS mutants, the mechanisms that lead to temperature sensitivity are not...
1h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntroduction: there is growing evidence that the IFN- -related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN- in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the non-canonical NF-kB pathway and its upstream kinase, NIK.Methodology: we developed...
1h
Contributor : Amanda MacLeodSeries Type : Expression profiling by arrayOrganism : Homo sapiensIL-27 plays a pivotal role in regulating complex immune responses. To evaluate the role of IL-27 in modulation in the expression of cellular and innate immunity-asscoiated genes in human epidermal keratinocytes (primary cells) and the monocytic THP-1 cell line (pre-treated with PMA) were stimulated with IL-27 and genome-wide expression of these cells were investigated utilizing microarray assay.
1h
Contributors : G M De Donatis ; T Passeron ; N Nottet ; A Paquet ; P BarbrySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntroduction: there is growing evidence that the IFN-γ-related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN-γ in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the...
1h
Contributors : Young-Ae Kim ; Gyeong Lim ; Jeong-Han Seo ; Sung Park ; Hee Lee ; Gyungyub GongSeries Type : Expression profiling by arrayOrganism : Homo sapiensTriple Negative Breast Cancer (TNBC) has been considered an aggressive and complex subtype of breast cancer. Current biomarkers used in breast cancer treatment are highly dependent on targeting ER, PR, or HER2 in clinical practice, which results in ttreatment failure and disease recurrence continue to be clinically challenging. In this...
1h
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below.
1h
Contributors : Anastasia Tsakmaki ; Patricia Fonseca Pedro ; Polychronis Pavlidis ; Bu’Hussain Hayee ; Gavin A BewickSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusObjective: Enteroendocrine cells (EECs) survey the gut luminal environment and co-ordinate hormonal, immune and neuronal responses to it. They exhibit well characterized physiological roles ranging from the control of local gut function to whole body metabolism, but little is known regarding...
1h
Contributors : Simone F Glaser ; Stefanie DimmelerSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusEndothelial cells play an important role in maintenance of the vascular system and the repair after injury. Under pro-inflammatory conditions, endothelial cells can acquire a mesenchymal phenotype by a process named endothelial-to-mesenchymal transition (EndMT), which affects the...
1h
Contributors : Xiaojiao Han ; Yunxing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Salix matsudanaComparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ABC transporters, K+ transporters/channels, yellow stripe-like proteins, Zinc regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW
1h
Contributors : Ana F Silbering ; Steeve Cruchet ; Karolina Bojkowska ; Sylvain Pradervand ; Richard BentonSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterHere, we tested the possibility that Drosophila peripheral olfactory system cells fated to die might represent a reservoir of potential neurons. Inhibition of PCD is sufficient to generate many new cells in the antenna that express neural markers. Transcriptomic and in situ analyses reveal that...
1h
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
1h
Contributors : Hui Zong ; Kevin Janes ; Maojin YaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe used RNA-sequencing technology for high-throughput profiling of tumor-derived astrocytes. Laser capture microdissection of individual cells was performed on an ArcturusXT LCM system (Applied Biosystems) with an infrared laser using CapSure HS LCM caps after optimization of laser power and duration. For each sample, 250 cells were microdissected per LCM cap...
1h
Contributors : Kared Hassen ; Larbi AnisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe report the application of single-molecule-based sequencing technology for high-throughput profiling of naive CD4 T cells. By sequencing this population in young and older donors, we describe the heterogeneity of Tscm CD4 cells based on differential engagement of Wnt pathways and inflammation.
1h
Contributors : G M De Donatis ; T Passeron ; N Nottet ; A Paquet ; P BarbrySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIntroduction: there is growing evidence that the IFN-γ-related cytokine signature plays a major role supporting the effect of pharmacological blockade of immune checkpoints. The expression of IFN-γ in cancer cells is repressed by several factors, among them a key role is played by the oncogene EZH2, which in turns is controlled by the...
1h
Contributors : Kared Hassen ; Larbi AnisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe report the application of single-molecule-based sequencing technology for high-throughput profiling of naive CD4 T cells. By sequencing this population in young and older donors, we describe the heterogeneity of Tscm CD4 cells based on differential engagement of Wnt pathways and inflammation.
1h
Contributors : L Chami ; P Barbry ; N Pons ; K Lebrigand ; A PaquetSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensOur aim was to compare gene expression profiles of nasal and bronchial epithelium in a same individual, notably at the level of Th2 inflammation.
1h
Contributors : Xue Li ; Huaiyong ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAutophagy is a cellular catabolic process that supports metabolism in response to stress. To identify gene expression that are modulated by autophagy in AT2 cells during BLM-induced lung injury, RNA-seq profiling were carried out with AT2 cells from Atg5f/f mice treated with PBS (AT2-PBS), Nkx2.1Cre; Atg5f/f mice treated with PBS (Atg5−/− AT2-PBS), Atg5f/f mice treated with...
1h
Contributors : Nadja Dinges ; Nastasja Kreim ; Violeta Morin ; Jean-Yves RoignantSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterlongitudinals lacking (lola) is among the most complex genes in Drosophila melanogaster, encoding up to 20 different protein isoforms and acting as a key transcription factor in axonal pathfinding and neural reprograming. To better characterize Lola function we have generated specific mutations in each isoform using...
1h
Contributor : Tatsuo FuruyamaSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo identify genes regulated by FOXO1 in HDLEC, we have empolyed whole genome microarray expression profiling. We identified CXCR4 as the most reduced gene after 72h of siRNA treatment for Foxo1 and the expression change was confirmed by RT-PCR and western blot.
3h
Contributors : Chia-Lin Wei ; Chew Y Ngan ; Harianto Tjong ; Chee-Hong WongSeries Type : Other ; Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusPolycomb repressive complex 2 (PRC2), a key regulator of metazoan development, induces transcriptional silencing by organizing repressive chromatin structures. To understand PRC2 associated genome topology, we performed chromatin interaction analyses focusing on...
5h
Contributors : Zhengyi Zhang ; Tamer SallamSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHeterogeneous nuclear ribonucleoproteins (hnRNPs) are a group of functionally versatile proteins that play critical roles in the biogenesis, cellular localization and transport of RNA. Although several lines of evidence link hnRNP abnormalities to neurodegenerative diseases and cancer their contribution...
9h
Contributor : Trevor ArcherSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe report whole genome chromatin immunoprecipitation followed by sequencing (ChIP-seq) of 3 different RNA Pol II CTD modifications in MCF-7 breast cancer cells treated with vehicle (UNTR) or the proteasome inhibitor MG132 for 4 (MG4H) or 24 (MG24H) hours. We find the non-phosphorylated form of RNA Pol II CTD accumulates at TSS of all expressed genes in proteasome inhibited...
10h
Contributors : Christopher C Nixon ; Maud Mavigner ; Gavin C Sampey ; Alyssa D Brooks ; Rae A Spagnuolo ; David M Irlbeck ; Cameron Mattingly ; Phong T Ho ; Nils Schoof ; Corinne G Cammon ; Greg K Tharp ; Matthew Kanke ; Zhang Wang ; Rachel A Cleary ; Amit A Upadhyay ; Chandrav De ; Saintedym R Wills ; Shane D Falcinelli ; Cristin Galardi ; Hasse Walum ; Nathaniel J Schramm ; Jennifer Deutsch ; Jeffrey D Lifson ; Christine M Fennessey ; Brandon F Keele ; Sherrie Jean ; Sean Maguire ; Baolin...
10h
Contributor : Trevor ArcherSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWe report whole genome chromatin immunoprecipitation followed by sequencing (ChIP-seq) of histone modifications in MCF-7 breast cancer cells treated with vehicle (UNTR) or the proteasome inhibitor MG132 for 4 (MG4H) or 24 (MG24H) hours. We find that MG132 treatment results in the spreading of the H3-trimethyl lysine 4 mark into gene bodies of a subset of induced genes in...
10h
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below.
10h
Contributor : Trevor K ArcherSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe 26S proteasome regulates degradation of many cellular proteins to maintain cellular homeostasis. Disruption of proteasome activity followed by dysregulation of tumor suppressors and oncogenes is rampant in many cancers, hence chemical inhibitors of the proteasome have utility as cancer therapeutics, although the underlying mechanisms of their effects in the clinic is poorly understood. We have employed...
10h
Contributors : Zhiyong Liu ; Chao Li ; Ken SuginoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe inner ear spiral ganglion neurons (SGNs) transmit sound information to brainstem. Although recent single-cell RNA sequencing studies confirm that SGNs are heterogeneous for different physiological functions, much remains to be known about their general transcriptomes, especially what genes are specifically expressed in SGNs but not in other inner ear cell...
12h
Contributors : Mark F Sabbagh ; Jeremy NathansSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusVascular endothelial cells (ECs) derived from the central nervous system (CNS) variably lose their unique barrier properties during in vitro culture, hindering the development of robust assays for BBB function, including drug permeability and extrusion assays. In previous work (Sabbagh et al., 2018)...
13h
Contributor : Carlos L ArteagaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPan-HER TKI neratinib has demonstrated clinical activity in patients with HER2-mutant cancers. However responses are heterogenoeus and not generally prolonged, suggesting de-novo and acquired resistance to neratinib. To study mechanisms of resistance to neratinib we generated neratinib resistant cells by gradual dose escalation until resistance was achieved and performed various analyses...
13h
Contributors : Alejandro Gozalo ; Maya CapelsonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogasterInteractions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding...
13h
Series Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogasterThis SuperSeries is composed of the SubSeries listed below.
13h
Contributors : Alejandro Gozalo ; Maya CapelsonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila melanogasterInteractions between the genome and the nuclear pore complex (NPC) have been implicated in multiple gene regulatory processes, but the underlying logic of these interactions remains poorly defined. Here, we report high-resolution chromatin binding maps of two core components of the NPC, Nup107 and Nup93, which reveal differential binding...
13h
Contributors : Kirsty Sawicka ; Caryn R Hale ; Robert B Darnell ; Jennifer C DarnellSeries Type : OtherOrganism : Mus musculusLoss of the neuronal RNA binding protein FMRP causes Fragile X Syndrome (FXS), the most common cause of inherited intellectual disability, yet it is unknown which brain regions and cell types within them contribute to disease pathophysiology. We used conditional tagging of FMRP and CLIP (cTag FMRP CLIP) to examine FMRP targets specifically in CA1 hippocampal neurons, a critical...
14h
Contributors : Kirsty Sawicka ; Jennifer C Darnell ; Robert B DarnellSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA-Seq from CA1 pyramidal neurons purified by FACS from 4-week-old mice.
14h
Series Type : Other ; Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below.
14h
Contributors : Kirsty Sawicka ; Robert B Darnell ; Jennifer C DarnellSeries Type : OtherOrganism : Mus musculusTRAP (translating ribosome affinity purification) from CA1 pyramidal neurons and cerebellar granule cells in wildtype and Fmr1 KO littermate pairs. These data show a global downregulation of FMRP targets in Fmr1 KO mice in these cell types.
14h
Contributors : Victoria E Hipolito ; Jacqueline A Diaz ; Kristofferson V Tandoc ; Christian Oertlin ; Johannes Ristau ; Neha Chauhan ; Amra Saric ; Shannon Mclaughlan ; Ola Larsson ; Ivan Topisirovic ; Roberto J BotelhoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe mechanisms that govern organelle remodeling remain poorly defined. Lysosomes degrade cargo from various routes including endocytosis, phagocytosis and autophagy. For phagocytes, lysosomes...
15h
Contributors : Thai Q Tran ; Shih Y Chen ; Fuu J TsaiSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensThere are the differential levels of methylation in the groups with and without complication to its control groups as non-diabetes and T2D without complication, two of which were classified into male and female, affects strictly the gene regulation to diabetic pathogenesis.To screen specific candidates for detecting classification of Type-2 Diabetes without or with...
15h
Contributors : Camille Wagner ; Lionel Spinelli ; Hugues LelouardSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSingle-cell RNA-sequencing was used to reveal LysoDC transcriptional plasticity and dynamics of differentiation
15h
Contributors : Haidong Shu ; Han Chen ; Suomeng Dong ; Yufeng FangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Phytophthora sojaeCentromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division. Despite functional conservation, centromeric sequences are diverse and usually repetitive across species, making them challenging to assemble and identify....
15h
Contributors : Devika Agarwal ; Cynthia Sandor ; Viola Volpato ; Tara Caffrey ; Rory Bowden ; Javier Alegre-Abarrategui ; Richard Wade-Martins ; Caleb WebberSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe describe the first human single-nuclei transcriptomic atlas for substantia nigra (SN), generated by sequencing ~ 17,000 nuclei from matched cortical and SN samples. We show that common genetic risk for Parkinson’s disease (PD) is associated with...
17h
Δεν υπάρχουν σχόλια:
Δημοσίευση σχολίου