Project description:Organoids were collected and signle cells were prepared in TrypLE. 10x Genomics Chromium was used for single cell capture and cDNA preparations according to the Single Cell 3' v3 Protocol recommended by the manufacturer.
Project description:Bulk RNA-sequencing experiments were performed to analyze the transcriptomic effects of such integrations into two newly established genomic safe harbor sites. Jurkat and HEK293T cells were edited to integrate CMV-mRuby expressing cassette into Rogi2 genomic safe harbor site using Cas9 RNP
Project description:We used single-cell RNA-seq to characterize the heterogeneity of the human Lin- stromal vascular fraction across five adipose depots. We mollecularly assessed Lin- SVF cells from subcutaneous, omentum, mesocolic, and perirenal fat depots, as well as gallbladder-associated fat using 10x Genomics.
Project description:In the study we show that a specific peripheral glial population, derived from boundary cap (BC) cells, constitutes a major source of mural cells for the developing vasculature. Using Cre-based reporter cell tracing and single cell transcriptomics, we show that BC cell derivatives migrate along the nerves and differentiate into pericytes and vascular smooth muscle cells in the skin. The switch from glial to mural molecular identity is initiated while the cells are still associated with nerves To further characterize this transition glial to vascular identity, we performed single cell transcriptomic analyses (scRNA-seq) on FACS-purified traced cells from dissociated E12.5 skin. Tomato-positive cells were isolated by FACS from embryonic skin at E12.5. Around 10,000 cells were loaded into one channel of the Chromium system using the V3 single cell reagent kit (10X Genomics) We analyzed 2527 single cell transcriptomes with a mean number of expressed genes per cell of 4,696. This study highlights the plasticity of BC derivatives and uncovers a novel, nerve-derived origin for skin mural cells.
Project description:Study of the emergence of the rare 2C like cell population upon Retinoic Acid treatment. Transcriptionally characterise the different cell populations emerging at different timepoints upon Retinoic Acid treatment and identify genes driving cell fate decisions.
Project description:CIARA (Cluster Independent Algorithm for the identification of RAre cell types) is tested on mouse embryonic stem cell treated for 24h with Retinoic Acid.
Project description:Red blood cells (RBC) depleted whole blood from COVID-19 patients and controls was harvested and processed in order to performed 10X single cell RNA-seq. For COVID-19 patients 2 samples 10 days a part were analyzed.
Project description:Study Description for ArrayExpress Submission: This study investigates cellular heterogeneity and mechanisms of gemcitabine resistance in pancreatic cancer using single-cell RNA sequencing of PANC-1 cells cultured in a 3D environment (and 2D control). Cells were seeded onto a decellularized porcine intestinal matrix to mimic the tumor microenvironment. The experiment analyzed transcriptional profiles before gemcitabine treatment, with particular attention to invasion and resistance states induced by TGFβ. Single-cell RNA-seq was used to map the transcriptional landscape of 3D pancreatic tumor tissues, capturing cell state transitions, differentiation trajectories, and resistance-associated profiles. The analysis identified cell cycle–dependent resistance signatures (late S to G2(/M) phase), tissue differentiation-associated states, and TGFβ-induced epithelial-to-mesenchymal transition (EMT) pathways contributing to chemoresistance. The dataset includes untreated samples with and without TGFβ stimulation, enabling identification of attractor states and transitional paths leading to gemcitabine resistance. This study provides insight into tumor cell plasticity and dedifferentiation in a 3D matrix environment, supporting early diagnostic and therapeutic research in pancreatic cancer.
Project description:The integrated stress response (ISR) is a conserved signaling pathway triggered by a variety of insults that include ER stress, mitochondrial stress, amino acid deprivation, and viral infection. The essential stress sensor and key effector of this pathway is eIF2B, and loss-of-function mutations in any of its 5 subunits can lead to Vanishing White Matter disease (VWM) in humans. We generated and characterized mouse models harboring different pathogenic mutations to model VWM and to understand the impact of chronic ISR activation on organismal and cellular physiology. Here, we performed single nuclei RNA-seq on the cervical/thoracic spinal cord from 3-month-old homozygous Eif2b1[N208Y] and WT mice, either maintained on a 30 mg/kg 2BAct diet or withdrawn from the diet for 3 days (n=3 per group). 2BAct is a small molecule eIF2B activator that can stabilize eIF2B and improve its function.
Project description:The integrated stress response (ISR) is a conserved signaling pathway triggered by a variety of insults that include ER stress, mitochondrial stress, amino acid deprivation, and viral infection. The essential stress sensor and key effector of this pathway is eIF2B, and loss-of-function mutations in any of its 5 subunits can lead to Vanishing White Matter disease (VWM) in humans. We generated and characterized mouse models harboring different pathogenic mutations to model VWM and to understand the impact of chronic ISR activation on organismal and cellular physiology. Here, we performed single nuclei RNA-seq on the cervical/thoracic spinal cord from 2.5-month-old homozygous Eif2b5[R191H] (n=3) and WT mice (n=3).