GSE267173 Short-chain fatty acids abrogate Japanese encephalitis virus-induced inflammation in microglial cells via miR200a-3p/ZBTB20/Ik βα axis
Contributors : Anirban Basu ; Atreye Majumdar ; Indira Priya Siva VenkateshSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusJapanese encephalitis virus (JEV), a member of the Flaviviridae family, is a leading cause of viral encephalitis in humans. Survivors of this infection often develop life-long neurological sequelae. Short-chain fatty acids (SCFAs) produced in the gut are vital mediators of the gut-brain axis. We aimed to study microRNA-based mechanisms of SCFAs in an in vitro model of JEV infection. N9 microglial cells were pre-treated with SCFA cocktail before JEV infectio...
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE267321 Gene expression profile at single cell level of non-malignant cells in KRAS syngeniec mouse tumor models harboring STK11 and/or KEAP1 co-muation
Contributors : Yu Qian ; Ferdinandos Skoulidis ; John V HeymachSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSTK11/LKB1 and KEAP1 mutations are associated with immunotherapy resistance. We employed KRAS syngeneic mouse cells (K) and generated KEAP1 loss (KK) or STK11/KEAP1 loss (KLK) by CRISPR/KO. Then we injected these tumor cells and collected the tumor for single-cell RNA-seq. Our aim is to analyze the impact of STK11 and/or KEAP1 deficiency on the immune microenvironment. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE267344 Cell-type transcriptomes for the choanoflagellate Salpingoeca rosetta
Contributors : David S Booth ; Fredrick LeonSeries Type : Expression profiling by high throughput sequencingOrganism : Salpingoeca rosettaTranscriptome profiles of four cell types from the choanoflagellate Salpingoeca rosetta : Slow Swimmers, Rosettes, Fast Swimmers, and Thecate (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Salpingoeca rosetta Source Type: research

GSE267400 Cut & Tag sequencing exhibited the chromosome binding regions of transcription factor IRF5 within murine bone marrow derived macrophages
Series Type : OtherOrganism : Mus musculusCUT&Tag technology represents a cutting-edge method for investigating protein-DNA interactions. Utilizing a hyperactive novel fusion enzyme (Hyperactive pG-Tn5 / pA-Tn5 Transposase), this technique, under antibody guidance, specifically targets and cleaves DNA sequences near target proteins. It boasts several advantages over traditional ChIP-Seq, including lower cell input requirements, enhanced signal-to-noise ratio, and improved repeatability. Employing this innovative approach, we examined the binding strength of interferon regulatory factor 5 in bone marrow-derived macrophages,...
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE267410 Comparative analysis of WT and XCR1 KO type 1 conventional dendritic cells [array]
Contributor : Yeon WooSeries Type : Expression profiling by arrayOrganism : Mus musculusXCR1 is known as a signature receptor of type 1 conventional dendritic cellsTo compare the transcriptomic differences of WT and XCR1 deficient type 1 conventional dendritic cells, we conducted microarry using type 1 conventional dendritic cells from WT and XCR1 KO mice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE267507 High-throughout sequencing of RAW264.7 cells treated with LPS and Harmine
Contributors : Yihui Zhai ; Xiaohui ZhengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAfter stimulation of RAW264.7 cells with LPS and Harmine, high-throughput sequencing technology was used to explore the changes in the inflammation level of RAW cells and the enrichment of signaling pathways after LPS and Harmine treatment, and to find an interesting target pathway. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE267508 CRISPR/Cas9 regulates EphA2-CDH1 axis to inhibit the migration of castration-resistant prostate cancer cells
Contributors : Song Yan ; Xiaojing Li ; Yiting Chen ; Peng Pan ; Ningfan Hu ; Lanyi Wei ; Yue Xiao ; Li Xiao ; Chaogang WeiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe ued CRISPR/Cas9 to knock out EphA2 gene in PC3 cells, and overexpress EphA2 gene in Du145 cells with overexpressed plasmids to explore the underlying mechanisms of EphA2 function in castration-resistant prostate cancer(CRPC) and clinical relevance, providing more evidence for EphA2 as a potential therapeutic target for CRPC. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267522 Lycorine attenuated proliferation and induced apoptosis on imatinib-resistant K562 cell by inhibiting autophagy.
Conclusion: In summary, K562/IM cells displayed heightened autophagy levels compared to K562 cells. Lycorine effectively impeded the proliferation of K562/IM cells through diverse mechanisms, including reduced autophagy, enhanced apoptosis, and induced cell cycle arrest. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267610 Multi-level proteomics profiling of virus restrictive and -permissive cellular environments reveal regulatory factors of virus infection
Contributors : Honglin Chen ; Quan GuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensVirus proliferation inside host cells relies on a diverse range of host machineries and is also restricted by the host through antiviral factors. The configuration of virus-dependency and antiviral factors determine the permissiveness of host cells to virus infection, however, overall differences between highly permissive and restrictive cellular states remain largely unexplored. Here we employed integrated omics analysis combining RNA-seq, proteomics, and phosphoproteomics to study determinants of ...
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE267624 Establishment and characterization of six canine hepatocellular carcinoma cell lines (Transcriptional changes induced by drug treatment with toceranib or sorafenib)
Contributor : Jayoung LeeSeries Type : Expression profiling by high throughput sequencingOrganism : Canis lupus familiarisHepatocellular carcinoma (HCC) is the most common malignant liver tumor in dogs. Although surgical resection is a major treatment option for canine HCC, there are no distinct strategies for unresectable tumor subtypes or adjuvant chemotherapy for tumors with positive margins. We aimed to establish and characterize novel HCC cell lines from canine patients. The cellular morphology, general growth features and tumorigenicity of the established cell lines were evaluated. We also examined the sensitivity o...
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Canis lupus familiaris Source Type: research

GSE267680 PanIN and CAF Transitions in Pancreatic Carcinogenesis Revealed with Spatial Data Integration [Xenium]
This study introduces a new imaging, spatial transcriptomics (ST), and single-cell RNA-sequencing (scRNA-seq) integration pipeline to characterize neoplastic cell state transitions during tumorigenesis. Our semi-supervised analysis pipeline was applied to examine pancreatic intraepithelial neoplasias (PanIN), the most frequent premalignant lesions that can develop into pancreatic adenocarcinoma (PDAC). Their strict diagnosis on FFPE samples has limited previous characterization of human PanINs within their microenvironment through single-cell approaches. We leverage unbiased whole transcriptome FFPE spatial profiling to en...
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE267869 Single-cell RNA-sequencing of human cytomegalovirus-infected humanized mice
In this study, we assessed the gene expression alterations of PBMCs at the single-cell level within HCMV-infected humanized mice, which sheds light onto the virus-host interactions in the context of HCMV infecton of humanized mice and provides a valuable dataset for the related researches. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 20, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE267482 Faecalibacterium prausnitzii-derived extracellular vesicles alleviate chronic colitis-related intestinal fibrosis by macrophage metabolic reprogramming II
In this study, oral administration of either live F. prausnitzii or its extracellular vesicles (FEVs) can markedly mitigate the severity of fibrosis in mice induced by repetitive administration of DSS. In vitro experiment revealed that FEVs were capable of directing the polarizati on of peripheral blood mononuclear cells (PBMCs) towards an M2b macrophage phenotype, which has been associated with anti-fibrotic activities. This effect of FEV was found to be stable under various conditions that promote the development of pro-fibrotic M1/M2a/M2c macrophages. Proteomics and RNA se quencing were performed to uncover the molecula...
Source: GEO: Gene Expression Omnibus - May 19, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE174737 Transcriptomics in the nucleus accumbens shell reveal sex- and reinforcer-specific signatures associated with morphine and sucrose craving
Contributors : Mayberry Hannah ; Bavley Charlotte ; Karbalaei Reza ; Peterson Drew ; Bongiovanni Angela ; Ellis Alexandra ; Downey Sara ; Toussaint Andre ; Wimmer MathieuSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusRNA-sequencing was performed using nucleus accumbens tissue from male and female rats following 1 or 30 days of morphine self-admininstration or sucrose self-adminnistration. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 19, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE203576 Tumor macrophages from rejecting and growing tumors
Contributor : Jarrod YeeSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophages in rejecting tumors have IFNg gene signature (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 19, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research