GSE235223 Transcriptional characterization of adjuvantly radio(chemo)therapy treated head and neck squamous cell carcinoma (HNSCC).
Contributors : Kristian Unger ; Julia He ß ; Martin Selmansberger ; Benedek Danko ; Horst Zitzelsberger ; Claus BelkaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe characterized n=134 HNSCC by Quantseq 3 ´-RNA-sequencing for their transcriptional profiles in order to analyze differential expression of clinically relevant subgroups, define transcriptionally defined molecular subgroups and to characterize the tumor microenvironment by gene expression devonvolution approaches. (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

GSE239661 Polyadenylation of mRNAs encoding secreted proteins by TENT5 family of enzymes is essential for gametogenesis in mice
Contributors : Micha ł Brouze ; Agnieszka Czarnocka-Cieciura ; Olga Gewartowska ; Monika Kusio-Kobiałka ; Kamil Jachacy ; Marcin Szpila ; Bartosz Tarkowski ; Jakub Gruchota ; Paweł Krawczyk ; Seweryn Mroczek ; Ewa Borsuk ; Andrzej DziembowskiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCytoplasmic polyadenylation plays a vital role in gametogenesis, however, the participating enzymes and substrates in mammals remain unclear. Using knockout and knock-in mouse models, we describe the essential role of 4 TENT5 poly(A) polymerases in mice fertility and gametogenesis. T...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE245699 High-throughput characterization of functional variants highlights heterogeneity and polygenicity underlying lung cancer susceptibility
Contributors : Harsh Patel ; Erping Long ; Alyxandra Golden ; Karen M Funderburk ; Jiyeon ChoiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGenome-wide association studies (GWAS) have identified multiple lung cancer risk loci including those that are distinct in the major histological types. However, most of these loci have not been functionally characterized. Here we employed massively parallel reporter assays (MPRA) to assess allelic transcriptional activity of risk-associated variants en masse. We tested 2,245 variants in 42 loci from 3 recent GWASs of East Asian and European...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE261810 LPS preconditioning enhances the therapeutic efficacy of MSC-derived exosomes in sepsis by altering miRNA expression profile
Contributors : Ting Zheng ; Sipeng Li ; Tao MaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusStudies have shown that stimulation of Mesenchymal stem cells (MSCs) with biophysical or biochemical cues could influence the contents and biological activities of subsequent MSC-derived exosomes. However, the underlying mechanisms have not been fully clarified. Here, we pretreated MSCs with lipopolysaccharide (LPS) and evaluated exosomes (LPS-Exo) therapeutic effects in sepsis. Analysis of exosomes activity revealed that LPS-Exo treatment improved sepsis to a greater extent than norma...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE266386 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies [ChIP-seq]
In this study, we identified CDK9 and CDK12, two transcription elongation regulators, as novel therapeutic targets for antagonizing the aberrant Hh pathway and overcoming SMOi resistance. CDK9 inhibition and CDK12 inhibition exhibited similarly potent anti-Hh activities when treating various SMOi responsive or resistant Hh-driven tumor models as previously reported BET inhibition or CDK7 inhibition. We also utilized SHH-subtype medulloblastoma (SHH-MB) as the representative Hh-driven cancer model to perform Super-enhancer (SE) analysis and elucidate the crucial roles of SE in Hh-driven oncogenesis and above-mentioned anti-...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE266389 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies [RNA-seq]
In this study, we identified CDK9 and CDK12, two transcription elongation regulators, as novel therapeutic targets for antagonizing the aberrant Hh pathway and overcoming SMOi resistance. CDK9 inhibition and CDK12 inhibition exhibited similarly potent anti-Hh activities when treating various SMOi responsive or resistant Hh-driven tumor models as previously reported BET inhibition or CDK7 inhibition. We also utilized SHH-subtype medulloblastoma (SHH-MB) as the representative Hh-driven cancer model to perform Super-enhancer (SE) analysis and elucidate the crucial roles of SE in Hh-driven oncogenesis and above-mentioned anti-...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE266391 Suppressing Aberrant Hedgehog Pathway and Overcoming Resistance to Smoothened Antagonists via Targeting Super-enhancer-driven Transcriptional Dependencies
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis 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 Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE266667 Human Cerebral Organoids: Cellular composition and subcellular morphological features
In this study, we have analyzed the cell types that compose hCOs of 45 days of culture (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

GSE267191 A single cell atlas of the mouse seminal vesicle
Contributors : Oliver J Rando ; Fengyun Sun ; Kathleen Desevin ; Yu FuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDuring mammalian reproduction, sperm are delivered to the female reproductive tract bathed in a complex medium known as seminal fluid, which plays key roles in signaling to the female reproductive tract and in nourishing sperm for their onwards journey. The majority of seminal fluid is produced by a somewhat understudied organ known as the seminal vesicle. Here, we report a single-cell RNA-Seq atlas of the mouse seminal vesicle, generated using tissues obtained from...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE267263 Increased ONECUT2 induced by Helicobacter pylori promotes gastric cancer cell stemness via AKT-related pathway
Conclusion: This study highlights a critical role played by ONECUT2 in promoting HP infection-associated GC by enhancing cell stemness through the PPP2R4/AKT/β-catenin signaling pathway. These findings suggest promising therapeutic strategies and potential therapeutic targets for GC treatment. Keywords: Helicobacter pylori; gastric cancer; prognosis; tumor stemness; ONECUT2 (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

GSE267285 Preweaning β-hydroxybutyrate elevation attenuates predisposition to metabolic dysregulation and impairs beige fat biogenesis in offspring of parents with high-fat diet-induced obesity
Contributor : Fu-Jung LinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusParental obesity (PO) predisposes offspring to an increased risk of obesity and type 2 diabetes in adulthood. We demonstrated that exogenous ketosis enhances blood ketone body β-hydroxybutyrate (βHB) concentration, regulating the adipogenic activity of parental obesity (PO) offspring and promoting beige adipogenesis to counteract obesity. Bulk RNA-seq analysis was performed on inguinal white adipose tissue-derived stromal vascular cells (iWAT-SVCs) obtained from offspri ng of control mice (Ln-F1) and obese mic...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE267318 Increase in ER-mitochondria contacts and mitochondrial fusion are hallmarks of mitochondrial activation during embryogenesis
Contributors : Anastasia Chugunova ; Roksolana KobylinskaSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioMitochondrial energy production is essential for development, yet the mechanisms underlying the continuous increase in mitochondrial activity during embryogenesis remain elusive. Using zebrafish as a model system for vertebrate development, we identify two sequentially acting mechanisms that could contribute to the rise in mitochondrial activity: an increased association between mitochondria and the endoplasmic reticulum (ER) at early stages, followed by the fusion of mitochondria...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE267560 Microenvironment Shapes Small Cell Lung Cancer Neuroendocrine States and Presents Therapeutic Opportunities [DMS273 SCLC cell lines]
Contributors : Desai Parth ; Thomas Anish ; Kumar RajeshSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSmall-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intra-tumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall comp...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267621 Clinical and molecular characterization of the cisplatin-vinorelbine chemotherapeutic regimen in HER2(-) metastatic breast cancer
Contributors : I-Wei Ho ; Yi-Ru Tseng ; Chun-Yu Liu ; Yi-Fang Tsai ; Chi-Cheng Huang ; Ling-Ming Tseng ; Ta-Chung Chao ; Jiun-I LaiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDespite rapid advances in treatment options, challenges still persist in advanced breast cancer. Bevacizumab is a VEGF-neutralizing antibody with proven efficacy in combination with chemotherapy for treatment of HER2 negative metastatic breast cancer (mBC). Vinorelbine, a semisynthetic vinca alkaloid, is a well-established and well tolerated chemotherapeutic in breast cancer. The combination of vinore...
Source: GEO: Gene Expression Omnibus - May 16, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267422 Myelin-reactive B cells exacerbate the severity of CD4+ T cell-driven CNS autoimmunity in an IL-23-dependent manner
Contributors : Mohamed Reda Fazazi ; Manu RangachariSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusB cells and T cells collaborate in multiple sclerosis (MS) pathogenesis. IgH[MOG]mice possess a B cell repertoire skewed to recognize myelin oligodendrocyte glycoprotein (MOG). Here, we show that upon immunization with the T cell-obligate autoantigen, MOG[35-55], IgH[MOG] mice develop rapid and exacerbated experimental autoimmune encephalomyelitis (EAE) relative to wildtype (WT) counterparts, characterized by aggregation of T and B cells in the IgH[MOG] meninges and by CD4+T helper 17...
Source: GEO: Gene Expression Omnibus - May 15, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research