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:Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This submission contains the Cell Ranger ARC processed outputs from single nuclei joint transcriptome- and chromatin accessibility-sequencing (10x Genomics). We also provide an integrated single nuclei transcriptomics dataset, comprised of malignant and tumour microenvironment cell type annotations.
Project description:We obtained human embryonic and fetal lungs from 5-22 pcw for scRNAseq and scATACseq analysis. To focus on epithelial differentiation and region specialization, we deeply sampled 15, 18, 20 and 22 pcw lungs and separated proximal and distal regions while leaving lungs at 5, 6, 9 and 11 pcw intact. These cell samples (except for one at 6pcw) were split and processed for both scRNAseq and scATACseq.