Project description:We undertook single-nucleus RNA sequencing to analyze primitive hematopoietic progenitors that circulate in embryonic mouse heart tubes at E10.5.
Project description:We used snRNA-seq to investigate an entire adult mammalian heart of BL6 mice. Whole hearts were harvested from 4 male mice (12 weeks) after cervical dislocation. The hearts were pooled and nuclei isolated using the Nuclei PURE Prep isolation kit (Sigma-Aldrich, Darmstadt, Germany) according to the manufacturer’s protocol. Sequencing was conducted by Genewiz (Leipzig, Germany) on the 10xGenomics system. Single nuclei were captured in droplet emulsions and snRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. RNA was controlled for sufficient quality on an Agilent 2100 Bioanalyzer system and quantified using a Qubit Fluorometer.
Project description:scRNA-seq was performed and data generated to examine the transcriptomic differences between PD-1/CTLA4 double-positive and double-negative CD4+ T cells in HIV patients.
Project description:We used snRNA-seq to investigate for the first time an entire adult mammalian heart. To avoid potential aberrations due to inbreeding, we relied on an outbred mice strain (Fzt:DU) (Dietl, G.; Langhammer, M.; Renne, U. Model simulations for genetic random drift in the outbred strain Fzt:DU. Arch. Anim. Breed. 2004, 47, 595–604). Whole hearts were harvested from 4 male mice (12 weeks) after cervical dislocation. The hearts were pooled and nuclei isolated using the Nuclei PURE Prep isolation kit (Sigma-Aldrich, Darmstadt, Germany) according to the manufacturer’s protocol. Sequencing was conducted by Genewiz (Leipzig, Germany) on the 10xGenomics system. Single nuclei were captured in droplet emulsions and snRNA-seq libraries were constructed as per the 10x Genomics protocol using GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. RNA was controlled for sufficient quality on an Agilent 2100 Bioanalyzer system and quantified using a Qubit Fluorometer. For further experimental details as well as computational scripts and results can be obtained from http://doi.org/10.15490/FAIRDOMHUB.1.STUDY.713.1.
Project description:In these experiments, we aimed to investigate the role of cardiomyocyte-specific deletion of the G-quadruplex resolvase Dhx36 in heart development and cardiomyocyte differentiation. To achieve this, we conducted multi-omics analysis using single-nuclei RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on hearts from postnatal day 7 (PD7) wild-type (WT) and Dhx36 conditional knockout (cKO) mice. Our findings reveal that Dhx36 plays a critical role in the development of the cardiac conduction system (CCS) and in the differentiation of both CCS and working cardiomyocytes
Project description:In these experiments, we aimed to investigate the role of cardiomyocyte-specific deletion of the G-quadruplex resolvase Dhx36 in heart development and cardiomyocyte differentiation. To achieve this, we conducted multi-omics analysis using single-nuclei RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) on hearts from postnatal day 7 (PD7) wild-type (WT) and Dhx36 conditional knockout (cKO) mice. Our findings reveal that Dhx36 plays a critical role in the development of the cardiac conduction system (CCS) and in the differentiation of both CCS and working cardiomyocytes
Project description:Single-nucleus multiomic data was generated from human fetal cochleae across 11, 14, and 16 post-conceptual weeks (PCW) using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression platform. Snap-frozen tissues were minced and lysed in ice-cold Nuclei Lysis Buffer, followed by filtration through a 40 μm strainer and centrifugation. Nuclear integrity was confirmed via trypan blue staining prior to mild permeabilization using 0.1× Lysis Buffer. After quenching and washing, nuclei were resuspended in Diluted Nuclei Buffer and concentration was adjusted to 4,000–8,000 nuclei/μL. Libraries were prepared following the standard 10X Multiome protocol for simultaneous gene expression and chromatin accessibility profiling. Sequencing was performed on the Illumina platform, producing paired-end reads. Raw data were processed through the Cell Ranger ARC pipeline (v2.0.0) with alignment to the GRCh38 human genome. The final output comprises paired gene expression matrices and chromatin accessibility peaks, both linked to the same individual nuclei through shared barcodes.
Project description:Aging is a major risk factor for cardiovascular diseases, yet the contribution of the lymphatic vasculature to cardiac aging remains largely unexplored. Here, we show that aging reduces lymphatic vessel density in human and mice hearts and induces morphological changes, including the formation of zipper-like, tighter endothelial junctions. These alterations are accompanied by immune cell infiltration, fibrinogen and amyloid accumulation, and myocardial edema. Experimental reduction of cardiac lymphatics in young mice, achieved by Flt4 (VEGFR3) depletion or overexpression of soluble Flt4, reproduces some age-related cardiac phenotypes, such as inflammation and impaired lymphatic integrity. Mechanistically, we found that aging induces the selective up-regulation of nuclear interleukin 33 (IL33) in lymphatic endothelial cells. In contrast to the extracellular, cardioprotective form of IL33, nuclear IL33 promotes lymphatic cell death and junctional remodeling. A targeted screen of pro-lymphatic factors identified VEGFC as an age-sensitive regulator that both declines in the aging heart and suppresses IL33. Cardiac Vegfc overexpression or Il33 silencing restores lymphatic vessel density, reduces macrophage infiltration, and improves tissue homeostasis in aged hearts. Collectively, these findings establish cardiac lymphatic dysfunction and VEGFC deficiency as key features of cardiac aging, highlighting potential therapeutic entry points for age-associated heart disease.
Project description:Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. Please cite De Jong et al., bioRxiv 2025 upon use. This submission contains the Cell Ranger ARC processed outputs from single nuclei joint transcriptome- and chromatin accessibility-sequencing (10x Genomics) for each multiome reaction generated as part of the GBM-space atlas. See README_cellranger_arc.md We also provide processed and annotated 10x multiome snRNA-seq and snATAC-seq objects across the dataset. See GBM_space_snRNA_README.md and GBM_space_ATAC_filtered_peaks_README.md respectively. Finally, we provide metacell-level aggregated snRNA-seq expression and snATAC-seq gene-activity scores derived from our GBM-space atlas, used for the epigenetic plasticity analysis in Saraswat M et al., bioRxiv 2025. See README_metacell.md.