GSE184793 The effect of over expression of StZFP2 on the wound response in Arabidopsis
Contributors : Susan D Lawrence ; Jonathan ShaoSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaExpression of genes in Arabidopsis Col-0 and 2 lines of overexpressing StZFP2 (OEEV47 1 and 2) were harvested without wounding (control) and 1h and 6h after wounding (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE74496 Trans-generatioanl epigenetic inheritance and resetting of an environmentally-triggered change in gene expression in C. elegans
Contributors : Adam Klosin ; Eduard Casas ; Cristina Hidalgo ; Tanya Vavouri ; Ben LehnerSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Caenorhabditis elegansTrans-generatioanl epigenetic inheritance and resetting of an environmentally-triggered change in gene expression in C. elegans (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE127660 CtBP2 ChIP-seq normal mouse liver
Contributor : Motohiro SekiyaSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusCtBP2 recruitment on genome in normal mouse liver (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE128145 Liver transcriptome regulated by CtBP2
Contributor : Motohiro SekiyaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusadenovirus mediated overexpression of wild-type CtBP2 and Rossmann fold mutant CtBP2 along with control GUS in dietary induced obese mice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE138101 Keap1 deletion-based Nrf2 activation accelerates mutant K-ras/p53-driven cholangiocarcinoma
Contributors : Tatsuhide Nabeshima ; Shin Hamada ; Keiko Taguchi ; Yu Tanaka ; Ryotaro Matsumoto ; Masayuki Yamamoto ; Atsushi MasamuneSeries Type : Expression profiling by arrayOrganism : Mus musculusAddition of liver-specific Keap1 deletion to mice harboring mutant K-ras and p53 accelerated cholangiocarcinoma formation, with hallmarks of Nrf2 activation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE149699 Single Cell RNA Sequencing of Cultured Primary Tissue Cells.
This study represents the first characterization of CDCs by sc-RNAseq and unravels their age-dependent molecular differences. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE158666 Differential expression of Triggering Receptor Expressed on Myeloid Cells (Trem)-2 in tissue eosinophils
Contributors : Albert C Sek ; Caroline M Percopo ; Arun K Boddapati ; Michelle Ma ; Wendy E Geslewitz ; Julia O Krumholz ; Justin B Lack ; Helene F RosenbergSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNo longer regarded as simply end-stage cytotoxic effectors, eosinophils are now recognized as complex cells with unique phenotypes that develop in response to the local microenvironment. In our previous study, we documented eosinophil infiltration in association with characteristic muscle damage in the dystrophin-deficient (mdx) mouse model of Duchenne muscular dystrophy. In this ear...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE159291 Spt4 helps RNAPII pass the +2 nucleosome barrier in vivo
Conclusion: This work suggests that Spt4 regulates nucleosome positioning by a mechanism related to transcription and promotes RNAPII movement through nucleosome barriers, especially the barrier set by the +2 nucleosome. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Other Methylation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE169362 Screening bioactive food compounds in honey bees suggests curcumin blocks alcohol-induced damage to longevity and DNA methylation
Contributors : Erik M Rasmussen ; Kristine L Seier ; Ingrid K Pedersen ; Claus Kreibich ; Gro V Amdam ; Daniel M ünch ; John Arne DahlSeries Type : Methylation profiling by high throughput sequencingOrganism : Apis melliferaVarious bioactive food compounds may confer health and longevity benefits, possibly through altering or preserving the human epigenome. While bioactive food compounds are widely being marketed as ‘improving health and longevity’ by counteracting harmful effects of poor nutrition and lifestyle, claimed effects are often not adequately documented. Using the honey bee (Apis mellifera) as a...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Apis mellifera Source Type: research

GSE171000 Targeting circRNA TFRC in bladder cancer alleviates urinary tract infections by reducing erythroid progenitor cells
Contributors : Kang Wu ; Song WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusthe same population of EPCs was detected in bladder cancer patients. The EPCs, whose function could be reversed via anti-CD71 treatment, were induced by the circRNA TFRC (circular RNA derived from the transferrin  receptor mRNA; cTFRC) in bladder cancer exosomes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184449 Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant
Contributor : Yohei HayashiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo evaluate global gene expression pattern changes between KLF4 L507A and WT during reprogramming, RNA-Seq was performed on the samples collected from reprogramming MEF infected with SeVdp vectors carrying KLF4 WT or L507A mutant. Original MEF and resulting miPSCs (mouse iPSCs) were also used as samples.RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs) by Lab Droid “Maholo” (Robotic Biology ...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184474 ANP32B-mediated repression of p53 contributes to maintenance of normal and CML stem cells
Contributors : Shuo Yang ; Yun YuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculuswe demonstrate that conditional deletion of acidic leucine-rich nuclear phosphoprotein 32B (ANP32B) in hematopoietic cells impairs repopulation capacity and postinjury regeneration of HSCs. Mechanistically, ANP32B forms a repressive complex with and thus inhibits the transcriptional activity of p53 in hematopoietic cells, and p53 deletion rescues the functional defect in Anp32b-deficient HSCs. Of great interest, ANP32B is highly expressed in leukemic cells from patients with chronic myeloge...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE184484 Early alterations in lipid metabolism in the spinal cord of SOD1 mice
This study aims to identify early lipid metabolic pathways altered before systemic metabolic symptoms in the spinal cord of mouse models of ALS. To do this, we performed a transcriptomic analysis of the spinal cord of  SOD1G93A mice at an early disease stage(p90) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184492 Differential gene regulation in DAPT-treated Hydra reveals candidate direct Notch signalling targets
Contributors : Jasmin Moneer ; Angelika BoettgerSeries Type : Expression profiling by high throughput sequencingOrganism : Hydra vulgarisIn Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes, we performed RNA-seq and identified genes that are differentially regulated in response to 48 h of treating the animals with the Notch inhibitor DAPT. To identify candidate direct regulators of Notch signalling, we profiled gene expression ...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Hydra vulgaris Source Type: research

GSE184495 IFNalpha-blockade during ART-treated SIV infection lowers tissue vDNA, rescues immune function, and improves overall health
Contributors : Louise Swainson ; Ashish A Sharma ; Peter Wilkinson ; Khader Ghneim ; Peter Hunt ; Joseph M McCune ; Rafick-Pierre SekalySeries Type : Expression profiling by high throughput sequencingOrganism : Macaca mulattaThe induction of type I interferons during acute viral infections drives local and systemic anti-viral responses. However, in chornic virus infection these type I interferon driven responses can be detrimental and can be characterized impaired immune responses (greater T cell exhaustion) and an overall decline in health outcomes. To parse out the role of type I IFN and assess the therapeutic impact of ...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Macaca mulatta Source Type: research

GSE184548 Progenitor-intrinsic metabolic sensing promotes hematopoietic homeostasis
We examined hematopoiesis in mice conditionally deficient in long-chain fatty acid oxidation (carnitine palmitoyltransferase 2, Cpt2), glutaminolysis (glutaminase, Gls), or mitochondrial pyruvate import (mitochondrial pyruvate carrier 2, Mpc2). While genetic ablation of Cpt2 or Gls minimally impacted most blood lineages, deletion of Mpc2 led to a sharp decline in mature myeloid cells. However, MPC2-deficient myeloid cells rapidly recovered due to a transient increase in myeloid progenitor proliferation. Competitive bone marrow chimera and stable isotope tracing experiments demonstrated that this proliferative burst was int...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184551 Macrophages from Rosa26-integrated Cas9-expressing C57BL/6 mice have a putative TRIF-mediated defect in the TLR-3/4 signaling
Contributors : Raktima Raychowdhury ; Matteo Gentili ; Ang Cui ; Lawrence D Schweitzer ; Bo Li ; Nir HacohenSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHere we report that the TLR4 ligand, lipopolysaccharide (LPS), and TLR3 ligand, polyinosinic:polycytidylic acid (poly (I:C)) failed to activate IRF3 or STAT1 in bone marrow derived macrophages (BMMs) isolated from two independently generated lines of Rosa26-integrated Cas9-expressing C57BL/6 (B6) mice. RNA-sequencing analysis reveals that hundreds to thousands of genes including interferon stimulated genes were differentially expre...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184649 Calycosin as a novel PI3K activator reduces inflammation and fibrosis in heart failure through AKT-IKK/STAT3 axis
Conclusion: Cal improves cardiac function against HF by inhibiting cardiomyocytes inflammation and fibroblasts fibrosis via activation of the PI3K-AKT pathway. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE184709 Identification of differentially expressed genes in Streptococcus agalactiae following phagocytic uptake and survival in THP-1 macrophage cells.
Contributors : Shannon D Manning ; Michelle L KorirSeries Type : Expression profiling by high throughput sequencingOrganism : Streptococcus agalactiaeThe goal of this analysis was to identify genes that promote survival of S. agalactiae within macrophages. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Streptococcus agalactiae Source Type: research

GSE184712 Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling [RNA-seq]
Contributors : Ying Xie ; Na Han ; Feng Li ; Lijuan WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFunctional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that RUNX2 and BGLAP osteogenic genes coordinate histone H3 lysine 36 dimethylation (H3K36me2) and transcriptional elongation factor Pol II to regulate chromatin dynamic and gene transcription during osteogenesis. Mechanistically, melatonin fa...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184713 Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling [ChIP-seq]
Contributors : Ying Xie ; Na Han ; Feng Li ; Lijuan WangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusFunctional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we demonstrate that RUNX2 and BGLAP osteogenic genes coordinate histone H3 lysine 36 dimethylation (H3K36me2) and transcriptional elongation factor Pol II to regulate chromatin dynamic and gene transcription during osteogenesis. Mechanistically...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE184714 Melatonin Enhances Osteoblastogenesis from Senescent Mesenchymal Stem Cells via NSD2 Mediated Chromatin Remodeling.
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. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE184735 Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases
Conclusions: We focused this first single-cell transcriptome study in granulomatous lung disease on macrophages. This study offers investigators cell-specific transcriptional changes (genes and networks/pathways) to consider mechanisms of granulomatous disease and as potential drug targets. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE184739 Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs)
Contributor : Yan LiuSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptional profiling of hematopoietic stem and progenitor cells comparing Bmi1 KO HSCs and MPPs to WT HSCs and MPPs (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE184751 Multiple regression analysis of a comprehensive transcriptomic data assembly elucidates mechanically- and biochemically-driven responses to focused ultrasound blood-brain barrier disruption - additional non-FUS controls
Contributors : Alexander S Mathew ; Catherine M Gorick ; Richard J PriceSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusFocused ultrasound (FUS) blood brain barrier disruption (BBBD) permits the noninvasive, targeted, and repeatable delivery of drugs to the brain. FUS BBBD also elicits secondary responses capable of augmenting immunotherapies, clearing amyloid- β and hyperphosphorylated tau, and driving neurogenesis. Leveraging these secondary effects will benefit from an understanding of how they correlate to the magnitude of FUS BBBD and are differentially affected by the mecha...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184758 Next Generation Sequencing Facilitates Quantitative Analysis of sorted lymphatic endothelial cells from the murine skin at 4 different time points of the day: ZT1, ZT7, ZT13, ZT19
Contributor : Julia Philippou-MassierSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare adhesion gene clusters and clock genes / biomarkers at different time points throughout the day in sorted murine lympahtic endothelial cells.Methods: RNA of sorted dermal LECs harvested in TriZol-LS was purified using Direct-zol RNA mini Prep Kit (ZymoResearch) following manufacturer ’s instructions. Isolated RNA was quantified using the Nanodrop (Therm...
Source: GEO: Gene Expression Omnibus - September 27, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE184745 miRNA changes after overexpression of LINC01126 in HepG2 cells
Contributors : Xianli Zhang ; Lili Zhao ; Yixiu ChenSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensTo identify putative miRNA targets for LINC01126, we overexpressed LINC01126 in HepG2 cells and carried out a microarray analysis. A total of 66 miRNAs present in the array demonstrated 1.5-fold upregulation or downregulation of expression upon LINC01126 transfection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE120481 The transcriptomes of PC3 cells with or without POH1 interference
Contributors : Wandong Yu ; Guowei ShiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTotal RNA was obtained from PC3 cells with or without POH1 interference to perform a High-throughput sequencing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120483 Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice I
Contributors : Nir Yogev ; Dev S Sams ; Federico Marini ; Andrea Cugurra ; Matthias KleinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to compare transcriptional changes evoked by T cells cross talk with meningeal macrophages. Furthermore, the role of specific T cell subsets or selected cytokine deficiency were used to evaluate their role in regulating such transcriptional changes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120485 Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice II
Contributors : Nir Yogev ; Dev S Sams ; Federico Marini ; Andrea Cugurra ; Matthias KleinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to compare transcriptional changes evoked by T cells cross talk with meningeal macrophages. Furthermore, the role of specific T cell subsets or selected cytokine deficiency were used to evaluate their role in regulating such transcriptional changes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120486 Next Generation Sequencing Facilitates Quantitative Analysis of Dura macrophage Transcriptomes post adoptive T cell reconstitution of RAG-1 deficient mice
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120530 FGF19 as a Surgical Factor Contributing to the Metabolic Effects of Gastric Bypass Surgery
Contributors : Alex M DePaoli ; Stephen A Harrison ; Mei Zhou ; Daniel D Kaplan ; James F Trotter ; Angelo H Paredes ; Steven C Hunt ; Ted D Adams ; Marc Learned ; Hui Tian ; Stephen J Rossi ; Lei LingSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusGastric bypass surgery has proven to be the most effective treatment in controlling hyperglycemia in severely obese patients with diabetes. Here we show that FGF19, a gut hormone, is rapidly induced by bypass surgery in rodents and humans. Administration of FGF19 achieves remission of diabetes through mechanisms beyond weight loss in animal models of diabe...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE135306 Targeting EYA2 tyrosine phosphatase activity in glioblastoma stem cells induces mitotic catastrophe
Contributors : Guoxin Zhang ; Jeremy N RichSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGlioblastoma ranks among the most lethal of primary brain malignancies, with glioblastoma stem cells (GSCs) at the apex of tumor cellular hierarchies. Here, to discover novel therapeutic GSC targets, we interrogated gene expression profiles from GSCs, differentiated glioblastoma cells (DGCs), and neural stem cells (NSCs), revealing EYA2 as preferentially expressed by GSCs. Targeting EYA2 impaired GSC maintenance and induced cell cycle arrest, apoptosis, and loss of self-renewal. EYA2 displayed n...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE156198 Histone demethylase Lsd1 regulates multiple repressive gene programs during T cell development
Contributors : Apratim Mitra ; Danny Stamos ; Lauren Clubb ; Jan Lee ; Dalal El-Khoury ; Paul E LoveSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEarly T cell development involves the stepwise maturation of thymus seeding progenitors that resemble multipotent hematopoietic stem/progenitor cells (HSPCs) into T-lineage committed cells. Analysis of the transcriptional profiles of developing thymocytes has shown that T-lineage commitment is associated with loss of early HSPC gene signatures and acquisition of T cell gene...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE159021 Neurofibromin (Nf1) controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors [RNA-seq]
Conclusions: The tumor suppressor Nf1 maintains the myogenic progenitor (MP) pool during postnatal muscle development. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE159022 Neurofibromin (Nf1) controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors [ChIP-seq]
Contributors : Xiaoyan Wei ; Sigmar StrickerSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe conclude that Nf1Myf5 MPs are driven towards quiescence and show metabolic reprogramming with severely inhibited glycolytic metabolism that, in turn impinges on H4K16ac decoration and expression of myogenic differentiation-related genes. ChIP-Seq analysis of freshly isolated p7 MPs showed apparently unaltered H3K4me3 levels between controls and Nf1Myf5 MPs, while H3K27me3 levels were globally reduced in Nf1Myf5 MPs. A reduction of H3K27me3 decoration was observed at genes assoc...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE159025 Neurofibromin (Nf1) controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors [MeDIP-Seq]
Contributors : Xiaoyan Wei ; Sigmar StrickerSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusWe conclude that the epigenetic alterations we observed in Nf1Myf5 MPs are in line with a shift towards a quiescent state, and that these alterations could contribute to impaired myogenic differentiation. Furthermore, hypermethylation and transcriptional downregulation of metabolic genes points towards changes in cellular energy metabolism in Nf1Myf5 MPs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE159026 Neurofibromin (Nf1) controls metabolic balance and Notch-dependent quiescence of murine juvenile myogenic progenitors
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE162669 Human tumor-associated macrophages from lung adenocarcinoma vs. alveolar macrophages from adjacent non-tumor tissue
Contributors : Jessica Hoppst ädter ; Anna Dembek ; Charlotte Dahlem ; Gilles Gasparoni ; Jörn Walter ; Hanno Huwer ; Martin Simon ; Marcel H Schulz ; Alexandra K KiemerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman tumor-associated macrophages (TAMs) were isolated from lung adenocarcinoma tissues and compared with alveolar macrophages (AMs) obtained from adjacent non-tumor tissues. For details, see Hoppst ädter et al., 2021 (doi:10.1016/j.ebiom.2021.103578). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE162698 Differentially polarized human monocyte-derived macrophages (M0, M1, M2/IL10, M2/IL4, TAM-like)
Contributors : Jessica Hoppst ädter ; Anna Dembek ; Charlotte Dahlem ; Gilles Gasparoni ; Jörn Walter ; Martin Simon ; Marcel H Schulz ; Alexandra K KiemerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn order to assess whether differences in the transcriptomic profile of human tumor-associated macrophages vs. alveolar macrophages from adjacent non-tumor-tissue (GSE162669) were caused by factors secreted by tumor cells, primary human monocyte-derived macrophages (MDMs) were polarized towards a TAM-like phenotype by cultivating them in tumor cell-conditioned medium. A genom...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178991 10X genomics single cell GEX and VDJ 5' sequencing of PBMC from Type 1 Diabetes patients treated with Treg therapy alone or plus low dose IL-2
Contributors : Shen Dong ; Jeffrey A BluestoneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground: A previous Phase I study showed that the infusion of autologous Treg cells expanded ex-vivo into recent onset Type 1 Diabetes (T1D) patients had an excellent safety profile, however, the majority of the infused Tregs could no longer be detected in the peripheral blood three months post-infusion (NCT01210664-Treg-T1D Trial). Interleukin-2 (IL-2) is a well-characterized cytokine that has been shown to enhance human Treg cell survival and expansion at low doses in vivo. Therefore, a ...
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE183406 Human hepatocellular carcinoma RNAseq data
Contributors : Yutaka Kurebayashi ; Kosuke Matsuda ; Akihisa Ueno ; Hanako Tsujikawa ; Ken Yamazaki ; Yohei Masugi ; Kathryn Effendi ; Hidenori Ojima ; Michiie SakamotoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThis is a series of RNAseq data obtained from the predominant region of 29 treatment-na ïve, surgically-resected human HCCs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE184575 Transcriptome analysis of dry cows transitioned from forage to 65% grain diet
This study aimed to explore the changes in global gene expression in the epithelial transcriptome during diet transition from forage to high-grain and the modulation through supplementation with phytogenic feed additives (PHY). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bos taurus Source Type: research

GSE184697 Transcriptome (RNA-seq) of HepG2 cells non-infected (NI) or infected (Inf.) with the pathogen Listeria monocytogenes (strain EGD-e)
Contributors : Natalie DESCOEUDRES ; Luc JOUNEAU ; Kevin GORRICHON ; H élène BIERNESeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensComparisons of gene expression profiles of human hepatocytes (HepG2) infected or not by the bacterium Listeria monocytogenes (strain EGD-e) for 72 hours and analysed by RNA-seq (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE184703 Expansion of Human Papillomavirus-Specific T Cells in Periphery and Cervix in a Therapeutic Vaccine Recipient Whose Cervical High-Grade Squamous Intraepithelial Lesion Regressed
Contributors : Mayumi Nakagawa ; Yong-Chen LuSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensSingle-cell TCR/transcriptome analysis for a peripheral blood lymphocytes (PBL) specimen was perform on a 10X Chromium instrument using a single-cell VDJ kit (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 25, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE184693 The protective role of hydrogen sulfide and its impact on gene expression profiling in rat model of COPD
Contributors : Yanjing He ; Yun Sun ; Chengcheng Liao ; Fan Lin ; Zhengyuan Xia ; Yongfen Qi ; Yahong ChenSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusTo investigate the role of H2S in Chronic obstructive pulmonary disease (COPD), a rat model of COPD was established by cigarette smoking (CS) and intratracheal instillation of lipopolysaccharide (LPS). Rats were randomly divided into 4 groups: Control, CS+LPS, CS+LPS+NaHS and CS+LPS+propargylglycine (PPG). Transcription profiling of lung tissue comparing Control with CS+LPS, CS+LPS with CS+LPS+NaHS, and CS+LPS with CS+LPS+PPG. The goal was to determ...
Source: GEO: Gene Expression Omnibus - September 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE148495 Generation of a functional, patient specific human thymus from induced pluripotent stem cell in vivo
Contributors : Stephan A Ramos ; Holger A RussSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusHere we describe a universal direct differentiation protocol that allows the generation of thymic epithelial progenitor cells (TEPs) from different iPSC lines. Upon transplantation into an athymic mouse model, TEPs further differentiate into thymic epithelial cells (TECs). TECs are functional and can facilitate the education of developing mouse T-cells. iPSC derived, patient specific TECs residing within grafts are indistinguishable from TECs present in human primary neonatal t...
Source: GEO: Gene Expression Omnibus - September 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE154959 Single cell RNA-seq profiling of murine endothelial cells in response to pulmonary hypertension
Conclusions: This study uncovers the murine endothelial cell transcriptomics changes in PAH at a high resolution, revealing novel candidates relevant to PAH. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160107 Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region
Contributors : Karim Abu Nahia ; Cecilia L WinataSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioThe atrioventricular canal (AVC) is the site where key structures responsible for functional division between heart regions are established, most importantly, the atrioventricular (AV) conduction system and cardiac valves. To elucidate the mechanism underlying AVC development and function, we utilized transgenic zebrafish line sqet31Et expressing EGFP in the AVC to isolate this cell population and profile its transcriptome at 48 and 72 hpf. The zebrafish AVC transcriptome exhibits hallmarks...
Source: GEO: Gene Expression Omnibus - September 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE161931 Transcriptomic study of heart tissue from diabetic cardiomyopathy mice
Contributors : Xin Huang ; Kunkai SuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo explore the key genes involved in spontaneous diabetic cardiomyopathy, db/db and BKS mice were used to examine the differently expressed genes in the related progresses. Briely, the heart transcriptome of db/db and BKS mice was correlated with the heart function, cardiomyocyte ultrastructure and histopathology characters. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - September 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research