GSE267355 Single cell RNA-sequencing of feline peripheral immune cells with V(D)J repertoire and cross species analysis of T lymphocytes
Discussion: Our study is the first to characterize the subtypes of circulating T cells utilizing an integrative approach of single cell RNA-sequencing, V(D)J repertoire analysis and cross species integration. Additionally, we also characterize s ubtypes in the myeloid cells expanding our understanding of the feline immune system. We have also demonstrated species immune cell relatedness which can provide an important foundation for further translational immunology, pathogenesis, translational treatments, and species-tropism of pathogens in veterinary medicine and research. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Felis catus Source Type: research

GSE267401 Spatial transcriptomics of colorectal cancer tissues
Contributors : Pariyada Tanjak ; Amphun Chaiboonchoe ; Thanawat Suwatthanarak ; Vitoon ChinswangwatanakulSeries Type : Expression profiling by genome tiling arrayOrganism : Homo sapiensWe study and report the whole transcriptome spatial profiling insights in colorectal cancer using the Visium spatial technique (Visium CytAssist, 10x genomics). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by genome tiling array Homo sapiens Source Type: research

GSE267402 Canid alphaherpesvirus 1 infection affects the gene expression and secretome profile of canine adipose-derived mesenchymal stem cells in vitro
Contributors : Marina Pri šlin ; Dragan BrnićSeries Type : Expression profiling by RT-PCROrganism : Canis lupus familiarisCanine adipose -derived mesenchymal stem cells (cAD-MSCs) demonstrate promising tissue repair and regeneration capabilities. However, the procurement and preservation of these cells or their secreted factors for therapeutic applications pose a risk of viral contamination, and the consequences on cAD-MSCs remain unexplored. Consequently, this research sought to assess the impact of Canid alphaherpesvirus 1 on the functional attributes of cAD-MSCs, including gene expression profiles and secretome c...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by RT-PCR Canis lupus familiaris Source Type: research

GSE267405 Retinal organoids with X-linked retinoschisis RS1 (E72K) mutation exhibit a photoreceptor developmental delay and are rescued by gene augmentation therapy
Conclusions The RS1 (E72K) mutation results in the photoreceptor development delay in ROs and can be partially rescued by the RS1 gene augmentation therapy. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267595 Genome-wide methylation studies in nasal epithelial cells using a custom Asthma & Allergy DNAm array
Contributors : Carole Ober ; William Wentworth-SheildsSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensWe performed an epigenome-wide association study (EWAS) of allergic sensitization using nasal epithelial cell DNA from 474 subjects. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE267653 An in vivo CRISPR screen in chick embryos reveals a role for MLLT3 in specification of neural cells from the caudal epiblast
Contributors : Ashley R Libby ; Tiago Rito ; Arthur Radley ; James BriscoeSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Gallus gallusDeveloping tissues rely on the coordinated differentiation of stem cell populations in dynamically changing environments. The formation of the vertebrate neural tube is a well characterized example, where stem cells in the caudal epiblast differentiate to neural tissue while transitioning through a changing landscape of signals: rostro-caudally from Retinoic Acid (RA) to Wnt/FGF and dorsal-ventrally from sonic hedgehog to BMP. Despite an understanding o...
Source: GEO: Gene Expression Omnibus - May 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Gallus gallus Source Type: research

GSE267628 Transcriptome analysis of JMML patients compare to healthy prenatal and postnatal samples.
Contributors : H élène Cavé ; Marion Strullu ; Aurélie Caye ; Chloé ArfeuilleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensJMML (Juvenile myelomonocytic leukaemia) is a leukaemia that only develops in young children and is thought to have a prenatal initiation. To study the relationship between JMML and normal ontogeny we studied the transcriptome of HPC (hematopoietic progenitor cells) sorted from sporadic JMML patients, healthy prenatal samples and from healthy age matched donors. Bulk transcriptome of sorted HPC reveals that some JMML samples cluster with prenatal sample...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE221499 Transcription factor shapes chromosomal conformation and regulates gene expression in bacterial adaptation
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Other ; Expression profiling by high throughput sequencingOrganism : Zymomonas mobilisThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing Zymomonas mobilis Source Type: research

GSE227998 TET2 Promotes Tumor Antigen Presentation and T Cell-Directed Tumor Cell Cytotoxicity Which is Enhanced by Vitamin C Treatment
Contributors : Meng Cheng ; Angel Chu ; Josh Welch ; Albert BaldwinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusImmune evasion by tumors is promoted by low T cell infiltration, an immunosuppressive tumor microenvironment, poor T cell activity directed against the tumor, and reduced tumor antigen presentation. We showed previously that tumor expression of the DNA dioxygenase TET2 enhances recruitment of T cells through activating the expression of CXCL9, 10 and 11. Vitamin C treatment was shown to increase these effects in a TET2 dependent manner. Using scSeq analysis, we sho...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE232347 ISRH-seq: a sensitive and robust methodology for R-loop profiling
Contributors : Wenli Zhang ; Ying Yang ; Jing Wu ; Mengqi LiSeries Type : OtherOrganism : Oryza sativaR-loops serve as key modulators in various biological processes in humans and plants.Current high-throughput methodologies for R-loop profiling have their own intrinsic pros and cons. Therefore, any robust, sensitive, and amenable methods, complementary and/or advantageous to existing methodologies, are much needed for advancing R-loop biology. We here present an RNase H based cleavage combined with DNA polymerase-mediated in situ biotin-dATP/dCTP labeling of newly synthesized DNA for sequencing, termed ISRH-seq, an an...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Other Oryza sativa Source Type: research

GSE232641 Evaluating Differential Tropism, Pathogenesis, and Antiviral Agents of Hemorrhagic Fever Renal Syndrome and Cardiopulmonary Syndrome Causative Hantaviruses: Andes virus (ANDV), Sin Nombre virus (SNV), and Hantaan virus (HTNV)
We report RNAseq analysis of control, calu3, astrocytes and cardiomyocytes cells under uninfected (mock) and Andes virus (ANDV), Sin Nombre virus (SNV), Hantaan virus (HTNV) infected and drug (synthetic 6AZA and Favipiravir, herbal Silymarin and Urolithin B) treated conditions (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE232642 Altered Chromatin State Drives Hypersocial Behaviors in Canids
We report supporting evidence of an E2F1-DNA binding peak concordant with the altered loop and higher expression of GTF2I exon 18. Additionally, we find altered looping with the canine LIMK1 gene and an increase in LAT2 expression within the loop. At a more global level, we discover differences in pathways regulating the extra-cellular matrix between samples of differential TE number. Our study emphasizes the role of chromatin architecture in social evolution. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Canis lupus familiaris Source Type: research

GSE232755 Defined conditions control the morphological dualism of rat primitive extraembryonic endoderm stem cells
We report two chemically defined conditions that differ by the addition of the cytokine Lif and the β-catenin-stabilizing drug Chir99021 and enable permanent self-renewal as mesenchymal and epithelial morphotypes, respectively. The morphotypes are interconvertible and differentiate equipotently. Surprisingly, the proliferation of both morphotypes requires Lif/Gp130/Stat3 signaling (autocrine in t he absence of added Lif) and non-canonical Wnt signaling (autocrine). Additionally, the epithelial version requires β-catenin for proliferation and morphology. Interestingly, the mesenchymal cells also express key epithelial mar...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE232837 Hydroxycitrate promotes muscle regeneration and delays early mortality in mice  
Contributors : Isabel Espadas ; Mar ía Ángeles Cáliz-Molina ; Raúl López-Fernández-Sobrino ; Concepción Panadero-Morón ; Alejandro Sola-García ; Mario Soriano-Navarro ; Enrique Martínez-Force ; Monica Venegas-Calderón ; Joaquin J Salas ; Franz Martín ; Benoit R Gauthier ; Clara Alfaro-Cerbelló ; David Martí-Agu ado ; Vivian Capilla-González ; Alejandro Martín-MontalvoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusATP-citrate lyase (ACLY) inhibitors have the potential of modulating central processes in protein, carbohydrate, and lipid metabolism, which can...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE234742 The Protective Role of Integrin α4β7 and Amphiregulin-Expressing Innate Lymphoid Cells in Lupus Nephritis
Contributors : Seungwon Ryu ; Hye Y KimSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusType-2 innate lymphoid cells (ILC2s) have emerged as key immune-response regulators in renal-inflammatory diseases such as lupus nephritis. However, the adhesion and migration of ILC2s, including in the homeostatic and diseased kidney, are poorly understood. By integrating transcriptomic profiling, flow cytometry, live-cell imaging, and in-vivo models, we showed that renal ILCs are retained in the homeostatic kidney by the adherence of their cell-surface integrin α4β7 to VCAM-1, E-cadherin or fib...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research