Find research datasets worth reusing

opencc-by-4.0Mar 2020View details →

Dataset related to article "Costimulatory Molecules and Immune Checkpoints Are Differentially Expressed on Different Subsets of Dendritic Cells."

Dendritic cells (DCs) play a crucial role in initiating and shaping immune responses. The effects of DCs on adaptive immune responses depend partly on functional specialization of distinct DC subsets, and partly on the activation state of DCs, which is largely dictated by environmental signals. Fully activated immunostimulatory DCs express high levels of costimulatory molecules, produce pro-inflammatory cytokines, and stimulate T cell proliferation, whereas tolerogenic DCs express low levels of costimulatory molecules, produce immunomodulatory cytokines and impair T cell proliferation. Relevant to the increasing use of immune checkpoint blockade in cancer treatment, signals generated from inhibitory checkpoint molecules on DC surface may also contribute to the inhibitory properties of tolerogenic DCs. Yet, our knowledge on the expression of inhibitory molecules on human DC subsets is fragmentary. Therefore, in this study, we investigated the expression of three immune checkpoints on peripheral blood DC subsets, in basal conditions and upon exposure to pro-inflammatory and anti-inflammatory stimuli, by using a flow cytometric panel that allows a direct comparison of the activatory/inhibitory phenotype of DC-lineage and inflammatory DC subsets. We demonstrated that functionally distinct DC subsets are characterized by differential expression of activatory and inhibitory molecules, and that cDC1s in particular are endowed with a unique immune checkpoint repertoire characterized by high TIM-3 expression, scarce PD-L1 expression and lack of ILT2. Notably, this unique cDC1 repertoire was subverted in a group of patients with myelodysplastic syndromes included in the study. Applied to the characterization of DCs in the tumor microenvironment, this panel has the potential to provide valuable information to be used for investigating the role of DC subsets in cancer, guiding DC-targeting treatments, and possibly identifying predictive biomarkers for clinical response to cancer immunotherapy.

opencc-zeroSep 2020View details →

Differentiation of parathyroid hormone expressing cells from human pluripotent stem cells

Abstract Differentiation of pluripotent stem cells into functional parathyroid-like cells would accelerate development of important therapeutic options for subjects with parathyroid-related disorders, from the design and screening of novel pharmaceutical agents to the development of durable cellular therapies. We have established a highly reproducible directed differentiation approach leading to parathyroid hormone (PTH) expressing cells from human embryonic stem cells (hESC) and induced pluripotent stem cells (iPSC). We accomplished this through the comparison of multiple different basal media, the inclusion of the CDK inhibitor PD0332991 in both definitive endoderm (DE) and anterior foregut endoderm (AFE) stages, and a 2-stage pharyngeal endoderm (PE) series. This is the first protocol to reproducibly establish PTH expressing-cells from human pluripotent stem cells and represents a first step towards the development of functional parathyroid cells with broad applicability for medicinal and scientific investigation.

opencc-zeroOct 2020View details →

Endocannabinoid signalling in stem cells and cerebral organoids drives differentiation to deep layer projection neurons via CB1 receptors

The endocannabinoid (eCB) system, via cannabinoid CB1 receptor, regulates neurodevelopment by controlling neural progenitor proliferation and neurogenesis. CB1 receptor signalling in vivo drives corticofugal deep layer projection neuron development through the regulation of BCL11B and Satb2 transcription factors. Here, we investigated the role of eCB signalling in mouse pluripotent embryonic stem cell-derived neuronal differentiation. Characterization of the eCB system revealed increased expression of eCB-metabolizing enzymes, eCB ligands and CB1 receptors along neuronal differentiation. CB1 receptor knockdown inhibited neuronal differentiation of deep layer neurons and increased upper layer neuron generation, and this phenotype was rescued by CB1 re-expression. Pharmacological regulation with CB1 receptor agonists or elevation of eCB tone with a monoacylglycerol lipase inhibitor promoted neuronal differentiation of deep layer neurons at the expense of upper layer neurons. Patch-clamp analyses revealed that enhancing cannabinoid signalling facilitated neuronal differentiation and functionality. Noteworthy, incubation with CB1 receptor agonists during human iPSC-derived cerebral organoid formation also promoted the expansion of BCL11B+ neurons. These findings unveil a cell-autonomous role of eCB signalling that, via CB1 receptor, promotes mouse and human deep layer cortical neuron development.

opencc-zeroSep 2019View details →

Data from: Differential requirements for the RAD51 paralogs in genome repair and maintenance in human cells

Deficiency in several of the classical human RAD51 paralogs [RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3] is associated with cancer predisposition and Fanconi anemia. To investigate their functions, isogenic disruption mutants for each were generated in non-transformed MCF10A mammary epithelial cells and in transformed U2OS and HEK293 cells. In U2OS and HEK293 cells, viable ablated clones were readily isolated for each RAD51 paralog; in contrast, with the exception of RAD51B, RAD51 paralogs are cell-essential in MCF10A cells. Underlining their importance for genomic stability, mutant cell lines display variable growth defects, impaired sister chromatid recombination, reduced levels of stable RAD51 nuclear foci, and hyper-sensitivity to mitomycin C and olaparib. Altogether these observations underscore the contributions of RAD51 paralogs in diverse DNA repair processes, and demonstrate essential differences in different cell types. Finally, this study will provide useful reagents to analyze patient-derived mutations and to investigate mechanisms of chemotherapeutic resistance deployed by cancers.

opencc-by-4.0Apr 2024View details →

Single-cell Roadmap dataset "Cardiac differentiation roadmap for analysis of plasticity and balanced lineage commitment" (Snabel et al.)

View the temporal single-cell transcriptomics data (UMAP, PCA, Heatmaps and Violin plots) using the Shiny App interface of iSEE (<a href="https://doi.org/10.12688/f1000research.14966.1">doi:10.12688/f1000research.14966.1</a>) for easy visualization of the single-cell data described in "Single-cell roadmap of cardiac differentiation identifies roles for ZNF711 and retinoic acid in balanced epicardial and cardiomyocyte lineage commitment" (Snabel et al., bioRXiv). For instructions on how to use this data, please visit https://github.com/Rebecza/scRoadmap_CardiacDiffs/.

Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14, BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of CNS-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE,  BM chimeric mice (CD45.2 Csf2rb-/-: CD45.1 Csf2rb+/+ and CD45.2 Ifngr1-/-: CD45.1 Ifngr1+/+) using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Lymph node-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Bone Marrow-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 using 10X Genomics platform. IFN-γ and GM-CSF control complementary differentiation programs in the monocyte to phagocyte transition during neuroinflammation.

Single-cell RNA sequencing of Blood-infiltrating HSC-derived phagocytes of Ms4a3Ai14 at onset and peak EAE using 10X Genomics platform. The sorted cells were loaded into 10x Genomics Chromium in parallel. Libraries were prepared as per the manufacturer's protocol (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol) and sequenced on an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=28, i7=8, R2=91) to a depth of around 50,000 reads per cell. Initial processing was done using Cell Ranger (v3.1.0) mkfastq and count (reads were aligned to GENCODE reference build GRCm38.p6 Release M23 with added tdTomato sequence for the dataset from Ms4a3Ai14 mouse and collapse UMIs). Starting from the filtered gene-cell count matrix produced by CellRranger's in-built cell calling algorithms, we proceeded with Seurat v4 workflow.

opencc-by-4.0Dec 2017View details →

H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells

In differentiated cells, aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal stem cells (MSCs) obtained from individuals aged 2 to 92 yr identified 18,735 hypermethylated and 45,407 hypomethylated CpG sites associated with aging. As in differentiated cells, hypermethylated sequences were enriched in chromatin repressive marks. Most importantly, hypomethylated CpG sites were strongly enriched in the active chromatin mark H3K4me1 in stem and differentiated cells, suggesting this is a cell type-independent chromatin signature of DNA hypomethylation during aging. Analysis of scedasticity showed that interindividual variability of DNA methylation increased during aging in MSCs and differentiated cells, providing a new avenue for the identification of DNA methylation changes over time. DNA methylation profiling of genetically identical individuals showed that both the tendency of DNA methylation changes and scedasticity depended on nongenetic as well as genetic factors. Our results indicate that the dynamics of DNA methylation during aging depend on a complex mixture of factors that include the DNA sequence, cell type, and chromatin context involved and that, depending on the locus, the changes can be modulated by genetic and/or external factors.

opencc-by-4.0Aug 2024View details →

Supplemental Data: Differential roles of kinetic on- and off-rates in T-cell receptor signal integration revealed with a modified Fab'-DNA ligand

Microscopy data and associated code for analysis. For more information refer to https://doi.org/10.1101/2024.04.01.587588.

opencc-by-4.0Sep 2024View details →

Single cell RNA-seq data from: Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma

Seurat object for single cell RNA-seq of 10 head and neck squamous cell carcinoma patients, epithelial cells only. From "Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma ". Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings suggest that APOBEC3A may play a functional role during keratinocyte differentiation and offer a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.

opencc-by-4.0Sep 2024View details →

CDK4/6 inhibitors display a class effect in inducing differentiation of neuroblastoma cells

Underlying and Extended data for the manuscript: "CDK4/6 inhibitors display a class effect in inducing differentiation of neuroblastoma cells", Ferguson et al (2024). Includes Underlying Data for Figures 1A-D, Figures 2A-F and Figures 3A-D and the Extended Data: Supplementary Information, data for Figures S1A-C and Movies S1 and S2.

opencc-zeroDec 2013View details →

Data from: Monocyte recruitment to the dermis and differentiation to dendritic cells increases the targets for Dengue virus replication

Dengue virus (DENV) causes the most prevalent arthropod-borne viral disease in humans. Although Aedes mosquitoes transmit DENV when probing for blood in the skin, no information exists on DENV infection and immune response in the dermis, where the blood vessels are found. DENV suppresses the interferon response, replicates, and causes disease in humans but not wild-type mice. Here, we used mice lacking the interferon-α/β receptor (Ifnar–/–), which had normal cell populations in the skin and were susceptible to intradermal DENV infection, to investigate the dynamics of early DENV infection of immune cells in the skin. CD103+ classical dendritic cells (cDCs), Ly6C– CD11b+ cDCs, and macrophages in the steady-state dermis were initial targets of DENV infection 12-24 hours post-inoculation but then decreased in frequency. We demonstrated recruitment of adoptively-transferred Ly6Chigh monocytes from wild-type and Ifnar–/– origin to the DENV-infected dermis and differentiation to Ly6C+ CD11b+ monocyte-derived DCs (moDCs), which became DENV-infected after 48 hours, and were then the major targets for virus replication. Ly6Chigh monocytes that entered the DENV-infected dermis expressed chemokine receptor CCR2, likely mediating recruitment. Further, we show that ~100-fold more hematopoietic cells in the dermis were DENV-infected compared to Langerhans cells in the epidermis. Overall, these results identify the dermis as the main site of early DENV replication and show that DENV infection in the skin occurs in two waves: initial infection of resident cDCs and macrophages, followed by infection of monocytes and moDCs that are recruited to the dermis. Our study reveals a novel viral strategy of exploiting monocyte recruitment to increase the number of targets for infection at the site of invasion in the skin and highlights the skin as a potential site for therapeutic action or intradermal vaccination.

opencc-by-4.0Nov 2022View details →

Dataset for puplication: Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing 1H-1H TOCSY NMR

Data set used in the publication: Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing 1H-1H TOCSY NMR. Abstract: In this work, the dynamic evolution of adipose tissue-derived human MSCs (AT-derived hMSCs) after fourteen days of cultivation, adiobocytes and osteocytes differentiation has been inspected based on 2D NMR TOCSY using machine learning techniques. Multi-class classification in addition to novelty detection of metabolites was established based on the profile of a control hMSCs sample at four days cultivation and successively detect the absence and the abundance of metabolites in differentiated MSCs following a set of 1H-1H TOCSY profiles. The uploaded files are: File:  metabolites_names.xlsx contain the names of the used metabolites. File: metabolites.xlsx  column 1: metabolite abbreviation column 2: 2D NMR TOCSY horizontal and vertical frequencies of metabolites in the control group at 4 days cultivation (Ct d4) column 3: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of cultivation (Ct d14) column 4: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of differentiation into adipocytes (AT d14) column 5: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after14 days of differentiation into osteocytes (OS d14) column 6: 2D NMR TOCSY horizontal and vertical standard frequencies of all metabolites measured at broadband high resolution 600.13 MHz NMR

opencc-by-4.0Feb 2022View details →

Hedgehog induced oxidative phosphorylation rescues the neuronal differentiation defect of human enteric neural crest cells underlying Hirschsprung disease

Hedgehog induced oxidative phosphorylation rescues the neuronal differentiation defect of human enteric neural crest cells underlying Hirschsprung disease

opencc-by-4.0Jan 2023View details →

ATAC-seq - Definitive endoderm differentiation of human pluripotent stem cells in G1 phase

Backup copy of the processed ATAC-seq data at http://ngs.sanger.ac.uk/production/endoderm/

opencc-zeroAug 2023View details →

SIRT2 is required for NaBT-induced CRC cell differentiation

Activation of the Wnt/β-catenin pathway is one of the hallmarks of colorectal cancer (CRC). Sirtuin 2 (SIRT2) protein has been shown to inhibit CRC proliferation. Previously, we reported that SIRT2 plays an important role in the maintenance of normal intestinal cell homeostasis. Here, we show that SIRT2 is a direct target gene of Wnt/β-catenin signaling in CRC cells. Inhibition or knockdown of Wnt/β-catenin increased SIRT2 promoter activity and mRNA and protein expression, whereas activation of Wnt/β-catenin decreased SIRT2 promoter activity and expression. β-catenin was recruited to the promoter of SIRT2 and transcriptionally regulated SIRT2 expression. Wnt/β-catenin inhibition increased mitochondrial oxidative phosphorylation (OXPHOS) and CRC cell differentiation. Moreover, inhibition of OXPHOS attenuated the differentiation of CRC cells induced by Wnt/β-catenin inhibition. In contrast, inhibition or knockdown of SIRT2 decreased, while overexpression of SIRT2 increased, OXPHOS activity and differentiation in CRC cells. Consistently, inhibition or knockdown or SIRT2 attenuated the differentiation induced by Wnt/β-catenin inhibition. These results demonstrate that SIRT2 is a novel target gene of the Wnt/β-catenin signaling and contributes to the differentiation of CRC cells.