GSE254390 CDK12 Loss Promotes Prostate Cancer Development While Exposing Vulnerabilities to Paralog-Based Synthetic Lethality
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 - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE254449 Single-cell profiling of mouse spleen myeloid cells
In this study, we identified a subset of neonatal monocytes with high expression of transmembrane protein Neuropilin-1 (Nrp1), termed Nrp1high monocytes. Nrp1high monocytes displayed potent immunosuppressive activity and their frequencies declined in age-dependent manner. Deletion of Nrp1 in myeloid cells aggravated the severity of neonatal inflammatory disease necrotizing enterocolitis (NEC). Adoptive transfer of Nrp1high monocytes led to remission of NEC. Mechanistic studies showed that Nrp1, via binding with its ligand semaphorin-4a (Sema4a), induced intracellular p38-MAPK/mTOR signaling and activated transcription fact...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE254524 ER-stress response in retinal M üller glia occurs significantly earlier than amyloid pathology in in the Alzheimer’s mouse brain and retina
In this report, we demonstrated pathological changes in retinal Müller glia significantly earlier than amyloid pathology in AD mous e models. By utilizing the knock-in NLGF mouse model, we surprisingly discovered an increase in reticulon 3 (RTN3) protein levels in the NLGF retina as early as postnatal day 30 (P30). Despite RTN3 being a canonically neuronal protein, this increase was noted in the retinal Müller glia, confirmed b y immunohistochemical characterization. Further unbiased transcriptomic assays of the P30 NLGF retina revealed that retinal Müller glia were the most sensitive responding cells in this mouse reti...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE254981 Auto-sumoylation of the Ubc9 E2 SUMO-conjugating Enzyme Extends Cellular Lifespan (RNA-Seq)
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: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research
GSE254993 The pulmonary inflammatory microenvironment at the time of exposure governs innate control of SARS-CoV-2 replication
Contributors : Paul J Baker ; Andrea C Bohrer ; Eduardo P Amaral ; Ehydel Castro ; Maryonne Snow-Smith ; Flor Torres-Ju árez ; Artur T Queiroz ; Eduardo F Rocha ; Sydnee T Gould ; Cassandra M Jordan ; Jaspal S Khillan ; Kyoungin Cho ; Reed F Johnson ; Daniel L Barber ; Bruno B Andrade ; Kerry L Hilligan ; Katrin D Mayer-BarberSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSARS-CoV-2 (SCV2) infection leads to diverse clinical outcomes ranging from asymptomatic to fatal disease. Co-morbidities, age and host genetics together with immune status affect disease severity. However, th...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE255351 Prophage-encoded methyltransferase upregulates virulence to drive adaptation in an outbreak of community-acquired methicillin-resistant Staphylococcus aureus [Harm analysis]
Contributors : Robert J Ulrich ; Bo ShopsinSeries Type : Expression profiling by high throughput sequencingOrganism : Staphylococcus aureusTo determine the effects of phage m ⏀11 on gene expression in 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
GSE256090 DNA damage hotspots for the Top2i "ICRF193"
We report the high-throughput identification of genomic hotspots for damage induction by ICRF-193, using γH2AX as a marker. We find that ICRF-193 primarily induces damage in repetitive sequences, which are known to reside in regions of heterochromatin, with a very small portion of damaged sites residing in regions of active genes in euchromatin. Overall, this study provides evidence that catalytic inh ibition of Top2 enzymes by ICRF-193, leads to induction of damage in the nuclear sub-compartments of heterochromatin. (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 Mus musculus Source Type: research
GSE256495 Convergent Epigenetic Evolution Drives Relapse in Acute Myeloid Leukemia
Contributors : Kevin A Nuno ; Armon Azizi ; Thomas K öhnke ; Caleb A Lareau ; Asiri Ediwirickrema ; M R Corces ; Ansuman T Satpathy ; Ravindra MajetiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensRelapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research
GSE257549 A male-essential microRNA is key for avian sex chromosome dosage compensation
Contributors : Amir Fallahshahroudi ; Mike J McGrew ; Henrick KaessmannSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Gallus gallusBirds have a sex chromosome system in which females are heterogametic (ZW) and males are homogametic (ZZ). The differentiation of avian sex chromosomes from ancestral autosomes entailed the loss of most genes from the W chromosome during evolution. However, to what extent mechanisms evolved that counterbalance the consequences of this extensive gene dosage reduction in female birds has remained unclear. Here we report functional in vivo and evolutionary analyse...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Gallus gallus Source Type: research
GSE260998 Germinal Center Dark Zone harbors ATR-dependent determinants of T-cell exclusion that are also identified in aggressive lymphoma – Visium_FFPE_Spatial_Trasciptomics_project
This study provides novel insights into signals controlling asymmetric T-cell distribution between DZ and LZ regions. We identify spatially-resolved DNA damage response and chromatin compaction molecular features precluding DZ T-cell infiltration. The DZ spatial transcriptional signature linked to T-cell immune evasion clustered aggressive Diffuse Large B-cell Lymphomas (DLBCL) for differential T cell infiltration. We reveal the dependence of the DZ transcriptional core signature on the ATR kinase and dissect its role in restraining inflammatory responses contributing to estabslish an immune-repulsive imprint in DLBCL. The...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research
GSE261004 Gene expression profiles of cells from PDOs of normal colon and colorectal cancers [RNA-Seq]
Contributors : Molong Qu ; Liang XiongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPhenotypic plasticity is a major driver of cancer progression, metastasis, and treatment resistance. However, the principles governing human cancer plasticity associated with poor prognosis remain poorly understood due to the lack of in vitro models. Here we identified a unique cancer cell state at single-cell resolution to predict poor prognosis across several human cancers with different clinical features, especially colorectal cancer (CRC) progression and metastasis, named the poor prognostic pl...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE261012 Single-cell gene expression profiles of cells from colorectal cancer and chemically induced PDOs [scRNA-Seq]
Contributors : Molong Qu ; Liang XiongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPhenotypic plasticity is a major driver of cancer progression, metastasis, and treatment resistance. However, the principles governing human cancer plasticity associated with poor prognosis remain poorly understood due to the lack of in vitro models. Here we identified a unique cancer cell state at single-cell resolution to predict poor prognosis across several human cancers with different clinical features, especially colorectal cancer (CRC) progression and metastasis, named the poor prognostic pl...
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research
GSE261184 Novel role of ALPI gene associated with constipation caused by complement component 3 deficiency
Contributors : Dae-Youn Hwnag ; Hee-Jin SongSeries Type : Expression profiling by arrayOrganism : Mus musculusTo pinpoint a distinctive gene associated with constipation resulting from C3 deficiency, we conducted microarray hybridization using total RNA extracted from the mid colon of C3 knockout (C3 KO) mice.Identification of causal genes through comparison of gene expression levels in mice induced with C3 deficiency. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research
GSE261280 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [ATAC-seq]
Contributors : Mitchell Conery ; James A Pippin ; Matthew C Pahl ; Struan F GrantSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo nominate identify tissues relevant to the etiology of bone mineral density we generated ATAC-seq in pediatric hMSC-osteoblasts, hFOB 1.19 cells (hFOBs), osteoclasts, and primary chondrocytes. Leveraging the results of this experiment, we designed a CRISPRi screen in hFOBs with scRNA-seq expression read out. The targets selected for the screen were informed by newly generated Capture-C and bulk RNA-seq from hFOBs. (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 Homo sapiens Source Type: research
GSE261281 Bioinformatics and single-cell CRISPRi-based screen reveals effector genes and implicates multi-tissue etiology for BMD [Capture-C]
Contributors : Mitchell Conery ; James A Pippin ; Matthew C Pahl ; Struan F GrantSeries Type : OtherOrganism : Homo sapiensTo nominate identify tissues relevant to the etiology of bone mineral density we generated ATAC-seq in pediatric hMSC-osteoblasts, hFOB 1.19 cells (hFOBs), osteoclasts, and primary chondrocytes. Leveraging the results of this experiment, we designed a CRISPRi screen in hFOBs with scRNA-seq expression read out. The targets selected for the screen were informed by newly generated Capture-C and bulk RNA-seq from hFOBs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research
