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: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:The experimental setup is aimed at understanding the function of the co-inhibitory receptor TIGIT in T cells. We compared sorted T cells (CD8+ T cells, CD4+Foxp3- T cells, CD4+Foxp3+ Tregs) from WT and TIGIT KO mice at steady state (naive mice) and following LCMV infection (day 10, LCMV clone 13). Cell were collected form spleen or lung.
Project description:Autoimmune regulator (Aire) orchestrates the display of peripheral self-antigens to T cells developing in the thymus, thereby playing a crucial function in the induction of immune tolerance. Mice lacking Aire develop multiorgan autoimmunity, but how that reflects on immune cells in the major lymphoid organs is not well understood. Here we used single cell RNA-seq to characterize immune cells isolated from the thymus, bone marrow (BM) and lymph node (LN) of four Aire-deficient (B6.AireC313X-/-) and four wild-type (WT) mice with two male and two female mice per genotype. B6.AireC313X-/- mice were generated and kindly provided by Yael Goldfarb and Jakub Abramson (previously described in Goldfarb et.al 2021, DOI: 10.1084/jem.20201076). The mice were 6-9 weeks old at the time of sacrifice. A total of nine sample types per individual mouse were generated in this study; immune cells isolated from three tissues; thymus, lymph node and bone marrow, where each tissue was used for GEX, TCR and BCR-seq. Information about individual, tissue, library type and lane are indicated in the sample name as follows: Genotype_MouseID_tissue_librarytype_lane ex. AireC313X_1_thymus_GEX_lane1
Project description:Characterization of human stem cell-derived microglia (hMG) that develop within vascularized human brain organoids under physiological conditions in vivo. We isolated tdT+/CD45+ hMG from five animals and three time points (6, 12 and 24 weeks post transplantation) using Fluorescence-activated cell sorting (FACS), following a strictly controlled ex vivo isolation procedure as previously described (Gosselin et al., 2017) and profiled those cells using single cell RNA sequencing.
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:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 91,922 nuclei in the mouse cerebellum across eleven developmental stages, from the beginning of neurogenesis (e10.5) till adulthood (P63). The study included two biological replicates per stage, one from each sex. Cerebelli were dissected as whole or in two halves, nuclei were extracted and profiled using 10x single-cell ATAC reagent kit (v1.0) and a Chromium controller. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).
Project description:This study used droplet-based snATAC-seq to profile the chromatin accessibility landscape of 19,204 nuclei in the opossum (Monodelphis domestical) cerebellum across two developmental stages (postnatal day 21 and adult). The study included two biological replicates per stage, one from each sex, and an additional adult sample enriched for white matter. Cerebelli were dissected in two halves, nuclei were extracted from one half and profiled using 10x single-cell ATAC reagent kit (v1.1) and a Chromium controller. The white matter enriched sample was dissected from coronal cerebellum slices. Libraries were sequenced using paired-reads on Illumina NextSeq 550 and initial data processing was performed using Cellranger ATAC (1.1).