Project description:To test the mechanism by which IGF1 is cardioprotective, we performed single cell RNA sequencing on myeloid cells isolated from the heart 3 days after myocardial infarction of mice with and without IGF1 treatment. Myocardial infarction was induced in C57Bl6/J mice by 45 min occlusion of the left anterior descending artery followed by 3 days of reperfusion. Animals of the IGF1 group (n=3) received 40 ng/g mature recombinant IGF1 subcutaneously as bolus at the beginning of reperfusion. In addition, IGF1 (1 µg/g/d) was administered continuously during reperfusion using micro-osmotic pumps (Alzet, 1003D) that were implanted subcutaneously. Control mice received vehicle (0.1% BSA). After 3 days hearts were digested and CD45+CD11b+ cells were isolated using FACS cell sorting. Each sample contained cells containing 1 control and 1 IGF1 treated mouse, labeled with TotalSeq hashtags. 16000 cells were used as input for the single-cell droplet libraries generation for each sample.
Project description:Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modelled this leukemic evolution through stepwise gene editing of GATA1s, SMC3+/- and MPLW515K providing 20 different trisomy or disomy 21 iPSC clones. Single cell analysis was performed on hematopoietic cells obtained from IPSC clones after 13 days of differentiation. Sample preparation was done at room temperature. Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded Gel Beads at a target capture rate of ~10,000 individual cells per sample. Captured mRNAs were barcoded during cDNA synthesis using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. All samples were processed simultaneously with the Chromium Controller (10X Genomics) and the resulting libraries were prepared in parallel in a single batch. We pooled all of the libraries for sequencing in a single SP Illumina flow cell. All of the libraries were sequenced with an 8-base index read, a 28-base Read1 containing cell-identifying barcodes and unique molecular identifiers (UMIs), and a 91-base Read2 containing transcript sequences on an Illumina NovaSeq 6000.
Project description:The spinal cord neural stem cell potential is contained within the ependymal cells lining the central canal. This neural stem cell potential is known to decline with age in the mouse. Here, we microdissected and dissociated into single cells the central canal region from the spinal cord of 4 young adult (3-to-4-month old) and 4 aged (18-to-19-month old) C57BL/6J mice to profile the transcriptomes of cells in and around the central canal using 10x Genomics technology.
Project description:Time course analysis of treatment-induced cell dynamics and comparison to non-targetting control. Treatment conditions were sequenced at 4h and 48h while the control was sequenced at 4h only. All samples had the epithelial compartment depleted before sequencing.
Project description:Molecular characterization of tissue-resident memory T cells cultured with or without donor-matched adult stem cell-derived intestinal organoids. Blood derived immune cells were also isolated and cultivated with autologous intestinal organoids for comparison and characterization. All conditions were derived from 3 human individuals and all samples were sequenced after 24h of in vitro culture. Data provides insights on circulating and tissue-resident immune cell populations, how these differentially interact with the epithelium and how these interactions shape both immune and epithelial cell states.
Project description:Macrophage colony-stimulating factor receptor (M-CSFR/CSF1R) signaling is crucial for the differentiation, proliferation, and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases, including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore, it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human-related diseases. Here, we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single-cell RNA sequencing. Our analysis of adult whole kidney marrow (WKM) hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non-overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease, mostly in cancerogenesis.
Project description:We performed single cell RNAseq to measure gene expression in different subsets of lung dendritic cells hyperglycaemic mice. We used streptozotocin model to achieve hyperglycaemia. Each sample contains cells from 4 different mice and hashing was done to allow disentangling which cell comes from which condition. Hashing was done with biolegend antibodies: Sample1: B0303: control 1, B0304 control 2, B0305 STZ 1, B0306 STZ 2 Sample2: B0303: control 3, B0304 control 4, B0305 STZ 3, B0306 STZ 4
Project description:Human embryonic stem cell-derived thyroid follicles were exposed for 3 days to a mixture of the sex hormones beta-estradiol (E2), 5-alpha-dihydrotestosterone (DHT) and progesterone (PG) that resemble the serum levels of human male and female (post-ovulation) of reproductive age. Afterwards, they were exposed for 1 day to the mixtures of sex hormones + 10 uM benzo[a]pyrene (BaP) or 10 uM PCB153. At the end of the treatment period, organoids were dissociated into single cell suspension and single cell RNA-Sequencing (scRNA-Seq) performed.
Project description:Human synovial Single cell RNA-seq was performed on three tissue samples from healthy donors. This experiment was done to explore the heterogeneity of cells in healthy human synovial joint and enabled the comparison of cellular states and composition to those of publicly available single cell RNA-seq datasets from psoriatic arthritis and rheumatoid arthritis patients. Human synovial cells were loaded immediately after tissue dissociation with up to 25,000 cells in a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev C). Libraries were sequenced as paired end (PE) 150 bp by Illumina sequencing to 65-80% saturation. Reads were mapped to the GRCh38 human genome (GENCODE) using the 10x Genomics Cell Ranger pipeline (7.2.0).