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894
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Dataset results
894 results for “Single-cell RNA-seq”
Single-Cell RNA-Seq Datasets of residual AML cells purifed from Patient Derived Xenograft bone marrow treated or not with venetoclax plus cytarabine
GEO Series GSE178912. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Single-Cell Multiomic Atlas of Human Cortical Development in Down Syndrome - Neural Cells in vitro Basic Characterisation Bulk RNA-seq Dataset
GEO Series GSE305135. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-seq in a model for HIV latency reversal
GEO Series GSE180133. Homo sapiens. 480 samples. Type: Expression profiling by high throughput sequencing.
Drosophila melanogaster female late third instar larval gonads single-cell RNA-Seq (scRNA-Seq) profiling
GEO Series GSE125948. Drosophila melanogaster. 3 samples. Type: Expression profiling by high throughput sequencing.
A single cell-based computational platform to identify chemical compounds targeting desired sets of transcription factors for cellular conversion [Single-cell RNA-seq]
GEO Series GSE162909. Homo sapiens. 1 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-seq data of sorted bone marrow CD19+B220+ B cells from Cyldflx/flx mice and Mb1Cre-Cyldflx/flx mouse models
<p>CYLD, a protein encoded by the Cyld gene, is a deubiquitinase involved in signalling events rather than proteasomal degradation. Mutations in CYLD are associated with familial cylindromatosis, leading to benign skin tumours. CYLD downregulates various solid and haematological tumours by negatively regulating signalling pathways like NF-κB, Wnt/β-catenin, and Notch. The most common Cyld splice variant encodes a 956 amino acid polypeptide with a catalytic domain at the carboxy-terminal, CAP-Gly domains at the N-terminal, and other domains in the central region. It interacts with various proteins, including tubulin, microtubules, and NEMO. CYLD is implicated in diverse functions such as cell proliferation, apoptosis, inflammation, spermatogenesis, and immune responses. Its role in B cell lymphopoiesis is less clear, with some studies showing increased B cell activation in Cyld-/- mice, while others suggest minimal impact on B cell maturation. To clarify CYLD's role in B cell lymphopoiesis, transgenic animals with B cell-specific catalytic inactivation of CYLD were created, revealing that CYLD plays a significant role in B cell maturation and function, with its disruption severely impeding B cell responses. Mb1Cre-Cyldflx/flx mice were generated by crossing a neo- derivative (<i>Cyldfl9/fl9</i> <i>neo-</i>) of the previously developed <i>Cyldfl9/fl9</i> mice25 with <i>Mb1Cre</i> mice33 (provided by Prof. M. Reth)34. In <i>Cyldfl9/fl9</i> mice, loxP sites flank the 9th exon and when recombination occurs in the presence of Cre recombinase, the ensuing exons, including the gene region encoding for the catalytic domain, are out of frame and not expressed. All mice were maintained under specific pathogen-free (SPF) conditions at the animal laboratory facility of the IRCCS Ospedale San Raffaele, Milan, Italy. Mice of experimental groups were age-matched (3 and 6 months), of both genders and, in most cases, littermates. All animal experiments were approved by the Animal Ethics Committee of the IRCCS Ospedale San Raffaele for compliance to European regulations and licensed by the National Veterinary Administration authorities of Italy. </p><p>For single-cell RNA sequencing, sorted bone marrow CD19+B220+ B cells were collected in RPMI medium (Euroclone, ECB2000) supplemented with 10% FBS (Euroclone, ECS0180L). Cell viability was then determined using Trypan Blue exclusion (Sigma-Aldrich, T8154-EA) and TC20 Automated Cell Counter (Bio-rad). 4000 cells were encapsulated using the Chromium Controller platform (10X Genomics) and libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics). Final libraries were sequenced according to the manufacturer's instructions on Novaseq6000. </p><p>The pertinent code can be found here: <a href="https://github.com/BiodataAnalysisGroup/Cyld-regulation-of-bcell-maturation">https://github.com/BiodataAnalysisGroup/Cyld-regulation-of-bcell-maturation</a></p>
Single-Cell RNA-seq Reveals FGF12 as a Prognostic Biomarker in Low-Grade Endometrial Stromal Sarcoma
<p><strong><span>Abstract </span></strong></p> <p><strong><span>Background: </span></strong><span>Low-grade endometrial stromal sarcoma (LG-ESS) is a rare uterine malignancy characterized by its complex tumor microenvironment (TME) and significant recurrence rates, posing challenges in accurate prognosis and effective treatment. Identifying prognostic biomarkers is essential to improve patient stratification and guide therapeutic strategies.</span></p> <p><span> </span></p> <p><strong><span>Methods: </span></strong><span>Using single-cell transcriptome analysis combined with H&E and multiplex immunofluorescence staining, we identified a subpopulation of tumor cells in LG-ESS and further validated the association of this subpopulation and its characteristic genes with LG-ESS prognosis by molecular characterization and bulk transcriptome data.</span></p> <p><span> </span></p> <p><strong><span>Results: </span></strong><span>Our analysis reveals multiple cellular subpopulations within the tumor tissue, particularly a tumor cell subpopulation among them which is associated with poor prognosis. Originating from normal stromal fibroblasts, this subpopulation appears to play a crucial role in TME remodeling, smooth muscle cell behavior, and potentially in tumorigenesis and metastasis. At particular interest in this subpopulation is the highly expressed FGF12 gene, which is significantly associated with a shortened survival time of ESS, highlighting its potential as a prognostic biomarker.</span></p> <p><span> </span></p> <p><strong><span>Conclusion: </span></strong><span>Our study reveals the complexity of TME within the LG-ESS and highlights the role that tumor cell subpopulations play in disease progression and patient prognosis. The identification of FGF12 as prognostic biomarkers suggests new approach for the personalized treatment and prognosis monitoring of patients. </span></p>
scINRB: single-cell gene expression imputation with network regularization and bulk RNA-seq data
<p>This data set contains simulation data and experimental data.</p> <p>The simulation data set includes simulated data with five different sizes, each of which contains five different dropout rates, generated by Splatter. Each .rds file contains simulated dropout data, true data and bulk data. </p> <p>The experimental data set includes CellBench benchmarking scRNA-seq datasets, ENCODE cell line data, and HCA data. </p>
Single-cell 5’ RNA-seq profiles of E16.5 forebrains in WT and Zfp661 knockout mice
GEO Series GSE231868. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-seq characterization of glioblastoma
GEO Series GSE224090. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-seq Reveals Unique Vascular Smooth Muscle Cell Phenotypes in Culture
GEO Series GSE79436. Mus musculus. 67 samples. Type: Expression profiling by high throughput sequencing.
T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile [single-cell RNA-seq]
GEO Series GSE228836. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
Performance comparison of high throughput single-cell RNA-Seq platforms in complex tissues
GEO Series GSE229765. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Lipid-accumulated reactive astrocytes promote seizure activity in epilepsy [single-cell RNA-seq]
GEO Series GSE190452. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Obesity Alters the Composition and the Activity of the Hematopoietic Stem Cell Compartment Through Dysregulation of Gfi1 Expression (single-cell RNA-Seq)
GEO Series GSE94087. Mus musculus. 285 samples. Type: Expression profiling by high throughput sequencing.
Characterization of differentiating adipose cells by high-throughput single-cell RNA-Seq
GEO Series GSE53638. Homo sapiens. 52 samples. Type: Expression profiling by high throughput sequencing.
The landscape of mouse epididymal cells defined by the single-cell RNA-Seq
GEO Series GSE151998. Mus musculus. 3 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-Seq of wild-type and Bcl6KO CD4+ T cell subsets during LCMV infection
GEO Series GSE184259. Mus musculus. 13 samples. Type: Expression profiling by high throughput sequencing.
Single-cell RNA-seq profiling reveals novel insights in immune-complex deposition and epithelium transition in IgA nephropathy
GEO Series GSE127136. Homo sapiens. 3620 samples. Type: Expression profiling by high throughput sequencing.
Single-cell transcriptomics reveals distinct molecular alterations of human renal cell carcinoma-derived endothelial cells that are stable in ex vivo primary culture [RNA-Seq]
GEO Series GSE237427. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.