Primitive erythroid and myeloid progenitors in mouse embryos
Ontology highlight
ABSTRACT: We undertook single-nucleus RNA sequencing to analyze primitive hematopoietic progenitors that circulate in embryonic mouse heart tubes at E10.5.
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: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.
Project description:Single-cell RNA sequencing of two human adrenal glands (obtained from renal cell carcinoma and pheochromocytoma cases) was performed to characterize the gene expression profile of aldosterone-producing cell clusters.
Project description:scRNA-seq was used to characterise hiPSC-derived kidney organoids differentiated within fully synthetic self-assembling peptide hydrogels of variable mechanical strengths and compare these to organoids differentiated within the animal-derived matrix, Matrigel. Organoids were matured in the respective matrices until day 24 of differentiation and 6 organoids per support matrix were then pooled and dissociated using the cold-active protease from Bacillus licheniformis. Cells were processed on the 10x Genomics Chromium platform using the Single-Cell 3’ v3.1 protocol. The NextSeq500 (Illumina) was used to sequence the libraries generated and initial processing of the data was carried out using the 10X Genomic Cell Ranger v3.1.0 pipeline.
Project description:A cryovial that contains frozen PBMCs (10^6 cells/vial) from each of 11 COVID-19 patients was thawed in 37oC water bath. Immediately after, thawed cells were transferred to 15-mL Falcon tube that contained 10 mL of cold culture medium. After centrifugation at 150g for 5 min, the cell pellets were resuspended in complete RPMI + 10% heat-inactivated FCS medium and plated onto 12-well plate at a concentration of 5 x 10^6 cells/3 mL/well. Then a peptide cocktail was added at a concentration of 5 μg/mL for 16hr in 5% CO2 37oC incubator. After 16-hour incubation, cells were washed 3 times and incubated for 10 minutes with Fc receptor block, following each sample was stained with a total of 6 HLA-A2+/peptide fluorescent tetramer (Tet) and pentamer (Pent) for 10 min. After cell washing at twice, each sample was stained with cell hashing antibodies for 20 min, respectively and then washed at three times and finally pooled. The combined cells were stained with CITE-seq and anti-human CD8 FACS antibody for 30 minutes. After cell washing at twice, viable HLA-A2+/peptide Tet/Pent positive CD8+ T cells were sorted by FACS Aria II. The scRNA-Seq libraries including GEX and CITE-seq libraries were prepared using the 10x Chromium single-cell 3’ reagent kits (v3.1 Chemistry), per manufacturer’s instructions. As a result, we have 2 separate groups of the single cell datasets. MKH datasets (MKH_GEX_... and MKH_FB...) contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 5 COVID-19 patients. MKK datasets contain RNA-seq outcomes of HLA-A2 restricted human CD8+ T cells against SARS-CoV-2 from 6 COVID-19 patients. Cell hashing and CITE-seq antibody information is available in the csv files.
Project description:To test the impact of nonsense-mediated decay (NMD) on BCR/TCR RNA sequences, we treated peripheral blood mononuclear cells (PBMCs) with cycloheximide to block NMD and analyzed treated and untreated cells by scRNA-seq with scVDJ-seq.
Project description:Acute Pten loss initiates prostate tumorigenesis characterized by cellular senescence response. Here we examine the cellular senescence response in epithelial individual cells, by single-cell RNA sequencing (scRNAseq) in Ptenpc-/- and Ptenpc-/-; Timp1-/- GEMMs. ScRNAseq analysis determines a cluster of senescent cells expressing the senescence-related genes. A significant positive correlation is observed between the senescence score and Bcl2 expression. This provides the rational for targeting senescent cells using Bcl2 inhibitor.