GSE261824 Threonine Phosphorylation of STAT1 Restricts Interferon Signaling and Promotes Innate Inflammatory Responses
Contributors : Tadamitsu Kishimoto ; Hozaifa Metwally ; Kazuki OkuyamaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSince its discovery over three decades ago, signal transducer and activator of transcription 1 (STAT1) has been extensively studied as a central mediator for interferons (IFNs) signaling and antiviral defense. Here, using genetic and biochemical assays, we unveil Thr748 as a conserved IFN-independent phosphorylation switch in Stat1, which restricts IFN signaling and promotes innate inflammatory responses following the recognition of the bacterial-derived toxin lipop...
Source: GEO: Gene Expression Omnibus - March 19, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE193082 Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [bulk RNA-Seq]
Contributors : Man Zhang ; Boyan Huang ; Jie Hu ; Xing PengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEmbryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate into trophoblas...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE193083 Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [scRNA-Seq]
Contributors : Man Zhang ; Boyan Huang ; Jie Hu ; Xing PengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusEmbryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate into trophoblas...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE193085 Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell [ChIP-Seq]
Contributors : Man Zhang ; Boyan Huang ; Jie Hu ; Xing PengSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEmbryonic stem cells (ESCs) can differentiate into all cell types of each of the embryonic germ layers. ESCs can also generate totipotent 2C-like cells and trophectodermal cells. However, these latter transitions occur at low frequency due to epigenetic barriers, the nature of which are not fully understood. Here, we show that mouse ESCs treated with sodium butyrate, an HDAC inhibitor, have a greatly increased 2C-like cell population and can transdifferentiate i...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE193087 Modulation of HDAC activity directly reprogramme embryonic stem cell to trophoblast stem cell
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 - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE210309 Pyrrole-based inhibitors of RND-type efflux pumps reverse antibiotic resistance and display antivirulence potential
Contributors : Nisha Mahey ; Rushikesh Tambat ; Ritu Kalia ; Rajnita Ingavale ; Nishtha Chandal ; Srajan Kapoor ; Dipesh K Verma ; Krishan G Thakur ; Sanjay Jachak ; Hemraj Nandanwar ; Akriti KodesiaSeries Type : Expression profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaEfflux pumps of the resistance-nodulation-division (RND) superfamily, particularly the AcrAB-TolC and MexAB-OprM, besides mediating intrinsic and acquired resistance, also intervene in bacterial pathogenicity. Inhibitors of such pumps could restore activities of antibiotics and curb bacterial virulence. Here, we identify py...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research
GSE222624 Transcriptional reprogramming by SPI1 (PU.1) modulates Alzheimer ’s disease phenotypes in mouse models
Contributors : Byungwook Kim ; Luke C Dabin ; Mason D Tate ; Hande Karahan ; Ahmad D Sharify ; Huan Sun ; Md M Al-Amin ; St éphanie Philtjens ; Daniel C Smith ; Dom J Acri ; Younghye Moon ; Mathias Jucker ; Junmin Peng ; Jungsu KimSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer ’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered befor...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE223666 Alternative splicing decouples local from global PRC2 activity
Contributors : Ivano Mocavini ; Niccolo Arecco ; Cecilia Ballare ; Luciano Di Croce ; Enrique BlancoSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPRC2 mediates epigenetic maintenance of gene silencing in eukaryotes via methylation of H3K27. This complex interacts with sets of accessory factors forming two distinct subtypes (PRC2.1 and PRC2.2) that differ in their action and chromatin targeting mechanisms. However, the underlying molecular mechanisms orchestrating PRC2 assembly are not yet understood. Here, we r...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research
GSE224163 A kinetic dichotomy between mitochondrial and nuclear gene expression processes
Contributors : Erik McShane ; Mary Couvillion ; Robert Ietswaart ; Gyan Prakash ; Brendan M Smalec ; Iliana Soto ; Autum R Baxter-Koenigs ; Karine Choquet ; L S ChurchmanSeries Type : OtherOrganism : Homo sapiensOxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS subunit biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including tran...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research
GSE225439 Bulk-RNA seq for Macrophages sorted from mouse lungs post influenza infection
Contributors : Gan Zhao ; Andrew E VaughanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate whether SPARCL1 affects lung macrophage polarization in vivoRNA sequencing (RNA-seq) of isolated lung macrophages (CD45+Ly6G-CD64+F4/80+) on day 20 post-influenza infection was used to further examine the consequences of EC overexpression of Sparcl1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE225669 Transcriptional reprogramming by SPI1 (PU.1) modulates Alzheimer ’s disease phenotypes in mouse models
Contributors : Byungwook Kim ; Luke C Dabin ; Mason D Tate ; Hande Karahan ; Ahmad D Sharify ; Huan Sun ; Md M Al-Amin ; St éphanie Philtjens ; Daniel C Smith ; Dom J Acri ; Younghye Moon ; Mathias Jucker ; Junmin Peng ; Jungsu KimSeries Type : Expression profiling by arrayOrganism : Mus musculusSPI1 (PU.1) was recently reported as a genetic risk factor of Alzheimer ’s disease (AD) in large-scale genome-wide association studies (GWAS). However, it is unknown whether PU.1 should be downregulated or increased to have therapeutic benefits. This is a critical question that must be answered before initiating any drug...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research
GSE229966 Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Other ; Expression profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE230942 Traumatic brain injury modifies adult hippocampal neural stem cell fate to promote neurogenesis at the cost of astrogliogenesis.
Contributors : Pascal Bielefeld ; Araks Martirosyan ; Arabo Apresyan ; Francisco Pestana ; Suresh Poovathingal ; Paul J Lucassen ; Juan M Encinas ; T G Belgard ; Matthew G Holt ; Carlos P FitzsimonsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe aimed to assess how TBI affects hippocampal NSCs and their subsequent commitment to the neuronal or astroglial lineages. Using a controlled cortical impact model of TBI, single cell RNA sequencing and spatial transcriptomics, we observed a cell population-specific increase in NSC-derived neuronal cells and a decrease in NSC-derived ast...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE233842 Transcription and DNA Replication Shapes DNA Break Dynamics in Long Neuronal Genes
Contributors : Vivien Ionasz ; Sergej Andrejev ; Lorenzo Corazzi ; Pei-Chi WeiSeries Type : OtherOrganism : Mus musculusTranscription and replication conflict (TRC) are one of the main driving forces for genome instability. Yet, TRC rarely been discussed without the context of DNA:RNA entanglement, rending the role of transcription in other TRC unclear . In neural stem and progenitor cells, genes encode protein regulating neuron adhesion are hotspots for recurrent DNA break clusters (RDC). While RDC-containing genes are all actively transcribed, most RDC lack DNA:RNA entanglement. We demonstrated that, through controll...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research
GSE234335 Single-cell trascriptiponal landscapes of bovine peri-implantation development
Contributors : Zongliang Jiang ; Hao Ming ; Giovanna ScatolinSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurusSupporting healthy pregnancy outcomes requires a comprehensive understanding of the cellular hierarchy and underlying molecular mechanisms during peri-implantation development. Here, we presented a single-cell transcriptome-wide view of the bovine peri-implantation embryo development at day 12, 14, 16 and 18, when most of the pregnancy failure occurs. We defined the development and dynamic progression of cellular composition and gene expression of embryonic disc, hypoblast, an...
Source: GEO: Gene Expression Omnibus - March 18, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bos taurus Source Type: research