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5,412 results for “Cell differentiation”
The transcription factor ETS1 is a master regulator of human NK cell differentiation
GEO Series GSE124104. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Quant-seq analysis of differential polyadenylation site usages in caused by different Pol II mutants with slow elongation rates in Flp-In-293 cells and dual inhibition of CDK12 and CDK13 by THZ531 HE
GEO Series GSE141375. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Identification of a new type of endocycle during multiciliated cell differentiation
GEO Series GSE201773. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
Fibrin Hydrogels Induce Mixed Dorsal/Ventral Spinal Neuron Identities During Differentiation of Human Induced Pluripotent Stem Cells
GEO Series GSE79442. Homo sapiens. 45 samples. Type: Expression profiling by high throughput sequencing.
Identification of microRNA-dependent gene regulatory networks driving human pancreatic endocrine cell differentiation [RNA-Seq III]
GEO Series GSE135197. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Data from: The lncRNA H19 mediates breast cancer cell plasticity during EMT and MET plasticity by differentially sponging miR-200b/c and let-7b
Metastasis is a multistep process by which tumor cells disseminate from their primary site and form secondary tumors at a distant site. The pathophysiological course of metastasis is mediated by the dynamic plasticity of cancer cells, which enables them to shift between epithelial and mesenchymal phenotypes through a transcriptionally regulated program termed epithelial-to-mesenchymal transition (EMT) and its reverse process, mesenchymal-to-epithelial transition (MET). Using a mouse model of spontaneous metastatic breast cancer, we investigated the molecular mediators of metastatic competence within a heterogeneous primary tumor and how these cells then manipulated their epithelial-mesenchymal plasticity during the metastatic process. We isolated cells from the primary mammary tumor, the circulation, and metastatic lesions in the lung in TA2 mice and found that the long noncoding RNA (lncRNA) H19 mediated EMT and MET by differentially acting as a sponge for the microRNAs miR-200b/c and let-7b. We found that this ability enabled H19 to modulate the expression of the microRNA targets Git2 and Cyth3, respectively, which encode regulators of the RAS superfamily member adenosine 5′-diphosphate (ADP) ribosylation factor (ARF), a guanosine triphosphatase (GTPase) that promotes cell migration associated with EMT and disseminating tumor cells. Decreasing the abundance of H19 or manipulating that of members in its axis prevented metastasis from grafts in syngeneic mice. Abundance of H19, GIT2, and CYTH3 in patient samples further suggests that H19 might be exploited as a biomarker for metastatic cells within breast tumors and perhaps as a therapeutic target to prevent metastasis.
Key physiological and metabolic characteristics for the differentiation of quiescent Salmonella's cells into persisters
<p>A prevalent tactic employed by bacteria to enhance their survival in challenging conditions, such as antibiotic exposure, involves entering a state known as quiescence. This state entails reversible arrest of cell growth, providing protection against various environmental stressors. Bacterial quiescence is of paramoubnt importance, particularly in <em>Salmonella enterica</em> serovar <em>Typhimurium</em> (<em>S. Typhimurium</em>), where the alternative sigma subunit of RNA polymerase, sigma S/RpoS, plays a crucial role in reshaping gene expression for stress resistance. Quiescent populations of bacteria can differentiate into persisters, surviving lethal antibiotic concentrations, which worsens antibiotic resistance issues. Understanding the mechanisms behind persister formation is crucial for drug development.</p> <p><strong>The study explores the interaction between sigma S and succinate dehydrogenase (Sdh) in persister formation at metabolic systems level.</strong></p> <p>Sdh, a membrane-bound complex connecting the TCA cycle and respiratory chain, is negatively regulated by sigma S, and its downregulation contributes to persister formation. This study aimed hence to understand the formation of antibiotic-resistant persister cells by characterizing the functional complementation of the Δ<em>sdh</em> mutation by the Δr<em>poS</em> mutation. The main findings are that i) persister formation is more efficient in rich medium than in minimal medium, with certain metabolic characteristics favoring persister formation in rich medium affected by the Δsdh mutation, ii) succinate accumulation in the Δ<em>sdh</em> mutant revealed by quantitative metabolomcs, with fumarate also accumulating, indicating the presence of an alternative pathway, iii) the Δ<em>sdh</em>Δ<em>rpoS</em> mutant metabolizes succinate despite the absence of Sdh, suggesting compensation by an alternative pathway negatively controlled by RpoS and, iv) the <em>frdABCD</em> locus encoding fumarate reductase appears to be involved in this alternative pathway, with biochemical studies needed to confirm its role.</p> <p>Phegnon, L., Uttenweiler-Joseph, S., & Létisse, F. (2024). EXTRAMETABOLOME ANALYSIS OF SALMONELLA corC MUTANTS BY NMR [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10908202</p>
Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation - Supplementary Data
<p>Genotype data for 19 cell lines from the Yoruba HapMap population that were used in this study, and summary statistics from QTL calling (see README.md in summary.zip).</p>
Coordination between metabolic transitions and gene expression by NAD + availability during adipogenic differentiation in human cells
<p>Adipocytes are the main cell type in adipose tissue, a critical regulator of metabolism highly specialized in storing energy as fat. Adipocytes differentiate from multipotent mesenchymal stromal cells through adipogenesis, a tightly controlled differentiation process involving closely interplay between metabolic transitions and sequential programs of gene expression. However, the specific gears driving this interplay remain largely obscure. Additionally, the metabolite nicotinamide adenine dinucleotide (NAD ⁺ ) is becoming increasingly recognized as a regulator of lipid metabolism, is postulated as a promising therapeutic target for dyslipidemia and obesity. Here, we explored the effect of manipulating NAD ⁺ bioavailability during adipogenic differentiation from human mesenchymal stem cells. We found a previously unappreciated strong repressive role for NAD ⁺ on adipocyte commitment, while a functional NAD+-dependent deacetylase SIRT1 appeared crucial for terminal differentiation of pre-adipocytes. Remarkably, repressing the NAD ⁺ biosynthetic salvage pathway during adipogenesis promoted the adipogenic transcriptional program, suggesting that SIRT1 activity during adipogenesis is independent of the NAD ⁺ salvage pathway, while two-photon microscopy and extracellular flux analyses suggest that its activation relies on the metabolic switch. Interestingly, SIRT1-directed control of subcellular compartmentalization of redox metabolism during adipogenesis was evidenced by two-photon fluorescence lifetime microscopy. Significance Statement Adipocyte differentiation occurs from mesenchymal stem cells through the adipogenic process, involving sequential activation of both transcriptional and metabolic programs in a tightly coordinated manner. However, how transcriptional and metabolic transitions reciprocally interact during adipogenic differentiation remains largely obscure. Here we describe that the metabolite NAD ⁺ suppresses adipogenesis through rewiring transcription, while a functional NAD-dependent deacetylase SIRT1 is essential for terminal differentiation of pre-adipocytes. Using two-photon fluorescence lifetime microscopy, we created a metabolic map of NADH and lipid content simultaneously in live cells and described a new role for SIRT1 in the control of compartmentalization of redox metabolism during adipogenesis. These findings advance our understanding to improve therapeutical approaches targeting the NAD ⁺ -SIRT1 axis as a treatment for obesity and dyslipemia.</p>
Continuous map of early hematopoietic stem cell differentiation across human lifetime
<p>This repository contains scCITEseq data generated from healthy stem and progenitor cells using the BD Rhapsody Single-Cell Analysis System.</p> <p><strong>File description:</strong></p> <p>1. RSEC-adjusted UMI count files generated using the BD Rhapsody Targeted Analysis Pipeline (v. 1.10 v. 1.10.1):</p> <ul> <li>Experiment_1_RSEC_MolsPerCell</li> <li>Experiment_2_RSEC_MolsPerCell</li> <li>Experiment_3_RSEC_MolsPerCell</li> <li>Experiment_4_RSEC_MolsPerCell</li> <li>Experiment_5_RSEC_MolsPerCell</li> <li>Experiment_6_RSEC_MolsPerCell</li> <li>Experiment_7_RSEC_MolsPerCell</li> <li>Experiment_8_RSEC_MolsPerCell</li> <li>Experiment_9_RSEC_MolsPerCell</li> <li>Experiment_10_RSEC_MolsPerCell<br><br></li> </ul> <p>2. Sample tag calls for each putative cell, output by the BD Rhapsody Targeted Analysis Pipeline (v. 1.10 v. 1.10.1):</p> <ul> <li>Experiment_1_Sample_Tag_Calls</li> <li>Experiment_2_Sample_Tag_Calls</li> <li>Experiment_3_Sample_Tag_Calls</li> <li>Experiment_4_Sample_Tag_Calls</li> <li>Experiment_5_Sample_Tag_Calls</li> <li>Experiment_6_Sample_Tag_Calls</li> <li>Experiment_7_Sample_Tag_Calls</li> <li>Experiment_8_Sample_Tag_Calls</li> <li>Experiment_9_Sample_Tag_Calls</li> <li>Experiment_10_Sample_Tag_Calls<br><br></li> </ul> <p>3. An excel file with all samples processed (cell type isolated, age group)</p> <ul> <li>Sample list</li> </ul> <p> </p>
Festem: Directly selecting differentially expressed genes for single-cell clustering analyses.
<p>Datasets related to article "Directly selecting differentially expressed genes for single-cell clustering analyses". Codes are available at <a href="http://github.com/XiDsLab/Festem_paper">https://github.com/XiDsLab/Festem_paper</a>.</p>
B Cell Differentiation in MS
ClinicalTrials.gov study NCT03744351. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Poorly Differentiated Adenocarcinoma With Signet Ring Cells of the Gallbladder Producing a High Level of Alpha-fetoprotein: a Case Report
ClinicalTrials.gov study NCT05559229. IPD Sharing: NO. Countries: 1. Publications: 0.
Research Development13(RD13)-02 Cell Injection in Patients With Relapsed or Refractory Cluster Of Differentiation 7(CD7)-Positive Hematological Malignancies
ClinicalTrials.gov study NCT05895994. IPD Sharing: NO. Countries: 1. Publications: 0.
Validation of Clara Cell Protein as a Novel Diagnostic Biomarker for the Differentiation of Cardiogenic Pulmonary Edema From Non-Cardiogenic Pulmonary Edema
ClinicalTrials.gov study NCT07338227. IPD Sharing: YES. Countries: 1. Publications: 0.
Efficacy of Biosimilar Filgrastim on the Mobilization of Hematopoietic Stem Cell CD34+ (Cluster of Differentiation 34) and on the Kinetic Engraftment
ClinicalTrials.gov study NCT02806791. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study of Brentuximab Vedotin as Therapy After Autologous Stem Cell Transplant in Cluster of Differentiation Antigen 30 (CD30) Positive Peripheral TCell Lymphomas
ClinicalTrials.gov study NCT04334174. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Protect and Improve Cluster of Differentiation 4 (CD4) Cells and B Cells Lymphocytes
ClinicalTrials.gov study NCT04770701. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Clinical Application Study of PET/CT for Differential Diagnosis of Non-small Cell Lung Cancer
ClinicalTrials.gov study NCT07026110. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Study Investigating Tarlatamab (AMG 757) in Patients With Metastatic/Locally Advanced Small-Cell Lung Cancer (SCLC) and Other Poorly Differentiated Neuroendocrine Carcinomas (NECs), With Biomarker Ana
ClinicalTrials.gov study NCT07016230. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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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.