Project description:We performed single-cell RNA sequencing with cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) on human bone marrow samples to characterize B cell populations. Cells were profiled using the 10x Genomics Chromium platform with simultaneous measurement of gene expression and antibody-derived tags (ADT), including IgD and IgM surface markers. This dataset enables integrated analysis of transcriptomic and protein-level features to resolve B cell developmental and functional states within the bone marrow microenvironment.
Project description:To study heterogenous cellular function and behaviors, we isolated individual cells from freshly resected and dissociated eight human neuroblastoma samples including 2 paired samples of primary tumors and bone marrow metastases, removed the inflammatory infiltrate and DAPI-positive dead cells , and performed single cell analysis using the 10x Genomics Chromium platform.
Project description:We report on the characterization of JMML hematopoietic stem and progenitor cells (HSPCs). In order to characterize the single cell heterogeneity in comparison to normal cord blood we preformed droplet based single cell RNA-seq of FACS sorted CD34+ cells using the 10x genomics platform. We identified distinct clustering of unique JMML HSPC populations in relation to cord blood control.
Project description:The malaria parasite Plasmodium replicates and differentiates in red blood cells of its host. The erythropoietic niches (spleen and bone marrow) are important but poorly understood reservoirs of asexual replication and sexual development. We aimed to understand how the parasite adapts to its host organ and a host cell level. For this, we performed single-cell RNA-seq (scRNA-seq) analysis on host and parasite cells derived from spleen, blood and bone marrow. Organs were harvested from two infected and one uninfected mice and parasite cells were enriched to about 50% by flow sorting (infected samples only). To identify host cells by surface expression (CITE-seq), cells were stained with barcoded antibodies targeting CD44 and CD71. Droplet-based scRNA-seq of these samples was performed using 10X genomics technology and cDNA was sequenced on Illumina.
Project description:We performed scRNA-seq analysis using the 10X genomics platform of mice following injection of mouse oropharyngeal carcinoma cell line MOPC in the flank of C57BL6/J to generate a model of murine oropharyngeal carcinoma. Here, we isolated bone marrow, spleen, blood and tumor from Gr1+and cKit+-enriched cells to investigate the dynamics of production across both sites of origin.
Project description:We performed scRNA-seq analysis using the 10X genomics platform of ApoE-/- mice fed for 16 weeks with high-fat diet (HFD). In these mice, we isolated brachiocephalic artery (BCA, digested), blood, bone marrow, spleen as well as perfusates of lung and liver at two times of the day (ZT1 and ZT13). For BCA cells, not-enriched cells and enriched cells (neutrophils, B- and T-cells, F4/80+ macrophages, CD31+ endothelial cells and CD31- stromal cells) were isolated and loaded for processing. For blood, bone marrow, spleen and the lung and liver perfusates, Lineage- Gr1+ were sorted together with enriched cKit+ cells.
Project description:Single nuclear RNA-sequencing was performed on spinal cord tissues from Tg(gfap:EGFP) zebrafish at 1 week post injury using the 10x Genomics platform.
Project description:To explore potential tissue origins of iILC2 during helminth infection, we performed single-cell RNA sequencing (scRNA-seq) of ILC2 and ILC progenitors using the 10x Genomics platform. Intestine draining mesenteric lymph nodes (Mes LN), lung, and bone marrow (BM) were collected 5 days post infection (dpi) with Nippostrongylus brasiliensis.
Project description:Over 16,000 nuclei were isolated from human postmartum brain frozen prefrontal cortex samples of alcoholic and control individuals. Libraries were prepared with 10X Genomics platform and sequenced using NovaSeq 6000.
Project description:We performed single-cell RNA sequencing (scRNA-seq) to characterize hematopoietic stem and progenitor cells (HSPCs) in a KrasG12D/+ mouse model of juvenile myelomonocytic leukemia (JMML). C-Kit⁺ HSPCs were enriched from the bone marrow of 6-week-old KrasG12D/+ and wild-type (WT) mice using CD117 MicroBeads and processed using the 10x Genomics Chromium Single Cell 3′ v3 platform. Libraries were sequenced on an Illumina NovaSeq 6000 system. Raw data were processed with Cell Ranger and analyzed using Seurat for quality control, dimensionality reduction, and clustering. HSPC subsets, developmental trajectories, and pathway activities were then analyzed to characterize leukemic alterations.