GSE250266 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [RNA-seq]
Contributors : Aur élie Hintermann ; Chase Bolt ; Lucille Lopez-Delisle ; Sandra Gitto ; Bénédicte Mascrez ; Denis DubouleSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
Gse250267 evolutionary co-option of an ancestral cloacal regulatory landscape with the emergence of digits and genitals
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Other ; Expression profiling by high throughput sequencingOrganism : Danio rerio ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing Danio rerio Mus musculus Source Type: research
GSE250367 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq]
Contributors : Aur élie Hintermann ; Chase Bolt ; Lucille Lopez-Delisle ; Sandra Gitto ; Bénédicte Mascrez ; Denis DubouleSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Third-party reanalysisOrganism : Danio rerio ; Mus musculusThe existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and succe...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Third-party reanalysis Danio rerio Mus musculus Source Type: research
GSE250368 EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [HiC-seq re-analysis]
Contributors : Aur élie Hintermann ; Chase Bolt ; Lucille Lopez-Delisle ; Sandra Gitto ; Bénédicte Mascrez ; Denis DubouleSeries Type : Other ; Third-party reanalysisOrganism : Danio rerioThe existence of homologies between fins and tetrapod limb skeletal parts as well as of the nature of those mechanisms underlying the transition of the former towards the latter, have been a rich source of discussion for more than a century. While the recent use of gene expression patterns to try and infer evolutionary scenarios has been a popular and successful approach, in particular the distribution of Hox transcript domains, ...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Other Third-party reanalysis Danio rerio Source Type: research
GSE250384 Wild type (WT) and Aconitate decarboxylase 1 knockout (Acod1-/-) BMDM treated with Imiquimod for 12h
Contributors : Eduardo Patino-Martinez ; Shuichiro Nakabo ; Kan Jiang ; Carmelo Carmona-Rivera ; Luz P Blanco ; Mariana J KaplanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe Krebs cycle enzyme Aconitate Decarboxylase 1 (ACOD1) mediates itaconate synthesis in monocytes and macrophages. Here, we explore the role of endogenous ACOD1-itaconate pathway in the activation of BMDM after imiquimod treatment. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE250438 Role of the TRIF-IFN-I pathway in Helicobacter-induced gastric cancer progression in an accelerated murine disease model
In this study, we found that H. felis-induced inflammation in Myd88-/- mice progressed to high-grade dysplasia, driven by activation of the type I interferon (IFN-I) signaling pathway and upregulation of its downstream targets, IFN-stimulated genes (ISGs). We also observed enrichment of IFN stimulated-response element (ISRE) motifs in the promoters of upregulated genes, further supporting the involvement of this pathway. In contrast, mice deficient in Toll/interleukin-1 receptor (TIR)-domain-containing adaptor inducing interferon- β (TRIF, TrifLps2) did not progress to severe gastric pathology after H. felis infection, im...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE252331 The Post-Septic Peripheral Myeloid Compartment Reveals Complex Diversity in Myeloid-Derived Suppressor Cells
Contributors : Efron A Phil ; Bacher RhondaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSepsis engenders distinct host immunologic changes that include the expansion of myeloid-derived suppressor cells (MDSCs). These cells play a physiologic role in tempering acute inflammatory responses but can persist in those patients who develop chronic critical illness. The origins and lineage of these MDSC subpopulations were previously assumed to be linear, discrete, and unidirectional; however, these cells exhibit a dynamic phenotype with considerable plasticity. Using Cellular Indexing of...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE252357 The 24-Hour Time Course of Integrated Molecular Responses to Resistance Exercise in Human Skeletal Muscle Implicates MYC as a Hypertrophic Regulator
Contributors : Sebastian Edman ; Ronald G Jones III ; Paulo R Jannig ; Kevin A Murach ; Ferdinand von WaldenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMolecular control of recovery after exercise in muscle is temporally dynamic. A time course of biopsies around resistance exercise (RE) combined with -omics is necessary to better comprehend the molecular choreography of skeletal muscle adaptation in humans. We collected vastus lateralis biopsies before and 30 minutes, 3-, 8-, and 24 hours after acute RE. RNA-sequencing defined the transcriptome and a time-point matched biopsy on...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE252480 Germinal Center Cytokines Driven Epigenetic Control of Epstein-Barr Virus Latency Gene Expression
Contributors : Yifei Liao ; Jinjie Yan ; Nina R Beri ; Lisa Giulino-Roth ; Ethel Cesarman ; Benjamin GewurzSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEpstein-Barr virus (EBV) persistently infects 95% of adults worldwide and is associated with multiple human lymphomas that express characteristic EBV latency programs used by the virus to navigate the B-cell compartment. Upon primary infection, the EBV latency III program, comprised of six Epstein-Barr Nuclear Antigens (EBNA) and two Latent Membrane Protein (LMP) antigens, drives infected B-cells into germinal center (GC). By i...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE252616 SOCS2 contributes to reduction of the third digit during development of the chicken forelimb
Contributors : Xiaoping Li ; Shanshan Li ; Shibin Bai ; Zhe WangSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusWe used the RCAS avian retrovirus to overexpress SOCS2 in the developing chicken limb buds and transcriptome sequencing (mRNA-Seq) revealed changes in expression of genes known to be associated with growth and development in forelimbs with overexpressed SOCS2. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Gallus gallus Source Type: research
GSE252660 Single cell RNA sequencing of lineage traced early postnatal myofibroblasts in the adult lung
Contributors : Rachana R Chandran ; Taylor Adams ; Daniel GreifSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEarly postnatal myofibroblasts are a key cell type involved in postnatal alveolarization. The majority of these cells undergo apoptosis post-alveolarization. However, some dedifferntaite and persist in the adult lung. We utilized single cell RNA seq. to understand transcriptomics of these persisted myofibroblasts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE252862 Prophage-encoded methyltransferase upregulates virulence to drive adaptation in an outbreak of community-acquired methicillin-resistant Staphylococcus aureus
Contributors : Robert J Ulrich ; Bo ShopsinSeries Type : Expression profiling by high throughput sequencingOrganism : Staphylococcus aureusTo determine the effects of phage adenine methyltransferase (pamA) on gene expression in WT USA300 (LAC*) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Staphylococcus aureus Source Type: research
GSE253055 Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan
We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2 Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. This increase is essential for the survival of aged cells an d CR-mediated ...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research
GSE254387 CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality [scRNA-Seq]
Contributors : Jean C Tien ; Yuping Zhang ; Yu Chang ; Yunhui Cheng ; Rahul Mannan ; Palak Shan ; Xiaoming Wang ; Sanjana Eyunni ; Caleb Cheng ; Brian Magnuson ; Lanbo Xiao ; Marcin Cieslik ; Abhijit Parolia ; Yi Bao ; Shuqin Li ; Alice Xu ; Fengyun Su ; Xuhong Cao ; Yi-Mi Wu ; Dan Robinson ; George Wang ; Ke Ding ; Arul M ChinnaiyanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBiallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration resistant prostate cancer (mCRPC). It remains unclear, however, whether C...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE254388 CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality [RNA-Seq]
Contributors : Jean C Tien ; Yuping Zhang ; Yu Chang ; Yunhui Cheng ; Rahul Mannan ; Palak Shan ; Xiaoming Wang ; Sanjana Eyunni ; Caleb Cheng ; Brian Magnuson ; Lanbo Xiao ; Marcin Cieslik ; Abhijit Parolia ; Yi Bao ; Shuqin Li ; Alice Xu ; Fengyun Su ; Xuhong Cao ; Yi-Mi Wu ; Dan Robinson ; George Wang ; Ke Ding ; Arul M ChinnaiyanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBiallelic loss of cyclin-dependent kinase 12 (CDK12) defines a unique molecular subtype of metastatic castration resistant prostate cancer (mCRPC). It remains unclear, however, whether C...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
