Ontology highlight
ABSTRACT:
PROVIDER: PRJNA930968 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23410581_1.fastq.gz | Fastqsanger.gz | |||
| SRR23410581_2.fastq.gz | Fastqsanger.gz | |||
| SRR23410582_1.fastq.gz | Fastqsanger.gz | |||
| SRR23410582_2.fastq.gz | Fastqsanger.gz | |||
| SRR23410583_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
Project description:Single-Cell RNA sequencing reveals the immune microenvironment and signaling networks in cystitis glandularis
| PRJNA934318 | ENA
Project description:Single-cell RNA sequencing reveals cellular dynamics in Hunner-type interstitial cystitis.
| PRJDB39959 | ENA
Project description:Metabolic dysfunction-associated steatohepatitis (MASH)-driven hepatocellular carcinoma (HCC) development is accompanied by the accumulation of immune cells within the hepatic microenvironment, yet its immunological networks remain obscure. Herein, we illustrate the profound reprogramming of the liver immune microenvironment during the transition from MASH to HCC by single-cell RNA sequencing (scRNA-seq).
2025-06-18 | GSE282630 | GEO
Project description:Combining single-cell and spatial transcriptomics for mapping different intestinal segments is still relatively absented, and the subtypes of intestinal stromal cells and their downstream signling also remain obscure. Our study provides a comprehensive view of 18 identified cell types across five mouse intestinal segments using single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with spatial transcriptomics reveals gene profiles along both segmental and crypt-villus spatial dimensions, including cell characteristics, interactions, signaling networks, extracellular matrix contributions, and functional coordination. Not only the different subtypes of intestinal immune cells were analyzed, but also a subtype of Pdgfra-high stromal cells, Gnai1+ stromal cells, was identified. These cells can support intestinal morphology and regulate the activities of goblet cells, Paneth cells, and intestinal stem cells via the activation of c-Jun and Wnt signaling. Thus, we have compiled a publicly available single-cell and spatial transcriptomics resource covering five intestinal segments to facilitate further research, particularly on stromal cell populations and intestinal microenvironment homeostasis.
2025-09-27 | GSE278251 | GEO
Project description:Single-cell RNA sequencing reveals compromised immune microenvironment in precursor stages of multiple myeloma
| PRJNA511584 | ENA
Project description:<p>Single-cell metabolomics reveals cell heterogeneity and elucidates intracellular molecular mechanisms. However, general concentration measurement of metabolites can only provide a static delineation of metabolomics, lacking the metabolic activity information of biological pathways. Herein, we developed a universal system for dynamic metabolomics by stable isotope tracing at the single-cell level. This system comprises an organic mass cytometry-based single-cell metabolomic platform and an automated metabolite quantification and untargeted metabolic flux data processing platform, providing an integrated workflow for dynamic metabolomics of living single cells. As a proof-of-concept, a total of 40 labeled metabolites were tracked in single breast cancer cells, enabling the global profiling and correlation analysis of metabolic activities across various metabolic pathways, as well as flow analysis of interlaced metabolic networks. The significance of metabolic activity profiling was underscored by a 2-deoxyglucose inhibition model, demonstrating delicate metabolic alteration within single cells which cannot reflected by concentration analysis. Significantly, the system combined with a neural network model successfully enabled the metabolomic profiling of direct co-cultured tumor cells and macrophages. This revealed intricate cell-cell interaction mechanisms within the tumor microenvironment and firstly identified versatile polarization subtypes of tumor-associated macrophages based on their metabolic signatures. Importantly, these findings are in line with the renewed diversity atlas of macrophages from genome features obtained through single-cell RNA-sequencing. The developed system facilitates a comprehensive understanding and opens a new avenue of single-cell metabolomics from both static and dynamic perspectives.</p>
2025-04-14 | MTBLS11091 | MetaboLights
Project description:<p>The endemic of SARS-CoV-2 underscores the imperative to elucidate its effects on pregnancy, particularly regarding the potential for vertical transmission and its influence on the early maternal-fetal interface, which remain insufficiently defined. To address this, we performed an extensive cohort study involving 761 pregnant women who voluntarily terminated the pregnancy during the first trimester. Analyses conducted using qRT-PCR, fluorescence in situ hybridization, and indirect immunofluorescence assay revealed minimal indications of SARS-CoV-2 infection within chorionic and decidual tissues. Although both tissues exhibited substantial expression of the viral entry receptors ACE2 and TMPRSS2, single-cell RNA sequencing analysis identified no cell populations with significant co-expression of these receptors. The restricted co-expression of viral entry receptors provides a mechanistic explanation for the rare occurrence of direct viral infection in placental tissues. The maternal systemic inflammatory response was notably attenuated relative to the classical cytokine storm, with only IL-31, IL-5, and GRO-α exhibiting elevated levels during acute infection. Furthermore, elevated IgG titers were inversely correlated with tumor necrosis TNF-β concentrations, suggesting a protective immunomodulatory function of IgG antibodies. Conversely, both bulk and single-cell transcriptomic analyses revealed pronounced, cell type-specific antiviral and immune responses within the placental microenvironment. A pervasive interferon-stimulated gene signature was identified, accompanied by emergence of M2-like macrophages with diminished antigen presentation capacity in convalescence. Importantly, maternal SARS-CoV-2 infection disrupted intercellular communication networks, notably impairing WNT and TGF-β signaling pathways to trophoblasts, thereby altering their differentiation trajectories. In summary, within this large first-trimester cohort, evidence for vertical transmission of SARS-CoV-2 was minimal. Nonetheless, infection substantially perturbs the placental immune milieu and trophoblast dynamics, which may adversely affect pregnancy outcomes.</p>
2026-03-05 | MTBLS13103 | MetaboLights
Project description:Single-cell RNA sequencing reveals immune microenvironment changes induced by Fe-Shikonin treatment in SCC7 tumors
| PRJEB106104 | ENA
Project description:The pathogenesis of interstitial cystitis/bladder pain syndrome (IC/BPS) remains incompletely understood. Bladder fibrosis is a significant histopathological feature of IC/BPS, particularly in non-Hunner-type IC (NHIC). Transient receptor potential cation channel subfamily C member 3 (TRPC3) is known to play a crucial role in myocardial and renal fibrosis. This study investigates the involvement of TRPC3 in bladder fibrosis associated with IC/BPS. A rat model of IC/BPS was established using cyclophosphamide (CYP, 50 mg/kg, intraperitoneally, every 3 days for 3 doses). Bulk RNA sequencing was used to identify differentially expressed transient receptor potential (TRP) channel genes in CYP-induced cystitis rats, whereas single-cell RNA sequencing was utilized to pinpoint the cell type predominantly expressing transient receptor potential cation channel subfamily C member 3 (TRPC3) . TRPC3 inhibition was achieved through intraperitoneal injection of Pyrazole 3 (Pyr3, 0.1 mg/kg or 1 mg/kg). Suprapubic mechanical allodynia was assessed using up-down method with von Frey filaments and micturition frequency was assessed by cystometry. The expression of TRPC3 and components of the transforming growth factor beta (TGF-β)/Smad signaling pathway (TGF-β, p-Smad2, and p-Smad3) in the bladder was analyzed by Western blot. Bladder fibrosis was assessed through Masson’s staining and detection of fibrosis markers (Vimentin, Collagen I, and Collagen III) using Western blot. The RNA and protein expression of TRPC3 was up-regulated in CYP-induced cystitis rats. TRPC3 inhibition led to significant improvements in suprapubic mechanical allodynia and reduced micturition frequency in CYP-induced cystitis rats. Western blot analyses revealed that markers of bladder fibrosis (Vimentin, Collagen I, and Collagen III) were markedly upregulated in CYP-induced cystitis rats. Masson’s staining showed an increased area of collagen fibers. Additionally, inhibition of TRPC3 resulted in significant downregulation of the TGF-β/Smad signaling pathway (TGF-β, p-Smad2, and p-Smad3) in CYP-induced cystitis rats. TRPC3 activation contributes to bladder fibrosis in IC/BPS. Inhibition of TRPC3 ameliorates suprapubic mechanical allodynia and micturition frequency in CYP-induced cystitis rats by downregulating the TGF-β/Smad pathway. TRPC3 represents a potential therapeutic target for managing bladder fibrosis in IC/BPS.
2025-03-31 | GSE293339 | GEO
Project description:By generating a paired single cell RNA-sequencing database of the tumor niche from 10 newly diagnosed MM patients, we created a unique dataset allowing the in-depth analyses of stromal-immune interactions within the tumor microenvironment (see related accession number). Using this database, we identified the presence of inflammatory stromal fibroblasts in the bone marrow of Myeloma patients.The stromal inflammation was associated with NF-κB signaling, and sources of IL-1β or TNFα were specific immune subsets previously shown to be altered in MM, suggesting the presence of an immune cell-mediated feed-forward loop of bone marrow inflammation in MM. By tracking inflammatory signatures over time in individual patients undergoing first-line treatment using bulk RNA sequencing, we show that bone marrow inflammation is not reverted by successful anti-tumor therapy (this dataset), suggesting a role for stromal fibroblasts and bone marrow inflammation in disease persistence or relapse. Raw sequencing data files will be deposited to EGA.
2021-02-01 | E-MTAB-9285 | biostudies-arrayexpress