Project description:The pituitary is the master endocrine gland regulating key physiological processes and houses a stem cell compartment. Despite the application of transgenic in vivo approaches, the pituitary stem cells' phenotype, biology, and role remain unclear. To tackle this question, organoids were developed as in vitro model to unravel pituitary stem cell biology. Pituitary organoids represent 3D cell structures that, under defined culture conditions, self-develop from SOX2-positive stem cells and recapitulate multiple hallmarks of pituitary stem cells. Here, we investigate the organoids' transcriptome starting from single-cell RNA-sequencing of organoids derived from pituitaries of neonatal, young-adult, middle-aged and elderly mice.
Project description:We profile single cells from patients with colorectum cancer using Chromium 3’ and 5’ single-cell RNA-sequencing. Patients EXT001, EXT009, and EXT012 from the KUL dataset were first analyzed by Lee et al., 2020, and the raw data are available in ArrayExpress under the accession codes E-MTAB-8410 and E-MTAB-8107. Patients EXT018, EXT048, EXT113, and EXT121 from KUL dataset were previously analyzed by Joanito et al., 2022. The raw data of those patients are available in EGA under the accession codes EGAD00001008584 and EGAD00001008585.
Project description:We profile single cells from patients with colorectum, ovary and breast cancer using various single-cell technologies, including Chromium 3’ and 5’ single-cell RNA-sequencing. <br>Note: Raw data files have been removed upon submitter's request.
Project description:Single-cell RNA sequencing was performed on retinal tissue from 12-week-old wild-type and Akimba (Ins2AkitaxVEGF+/-) mice, which are known to replicate features of clinical diabetic retinopathy. The aim of this study was to provide deeper insight into the complex network of molecular and cellular changes that underlie diabetic retinopathy by measuring the transcriptional changes that occur in the different cellular compartments of the degenerating diabetic mouse retina. Retinas (n=4 for Akimba, n=2 for wild-type) were isolated in ice-cold Dulbecco’s Modified Eagle Medium. After rinsing with Dulbecco’s Phosphate-Buffered Saline containing 2% fetal bovine serum, each retina was incubated with 1mL digestion buffer (2mg/mL collagenase-P, 200U/mL DNAse-I (Sigma-Aldrich) in M199 medium (Life Technologies) at 37°C for 10min. Retinal tissue was further dissociated by trituration and the suspension was filtered through a 40µm cell strainer and centrifuged for 5min at 300xg (4°C). Pooled retinal single-cell suspensions from wild-type and Akimba were counted on a Luna-FL Cell Counter (Logos Biosystems) and libraries were prepared with the Chromium Single-cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics) aiming for 5000 cells per library. Barcoded libraries were sequenced on an Illumina HiSeq4000 in 25-8-98 paired-end configuration. The transcriptome data for 9474 retinal cells were analysed, yielding 15 clusters corresponding to eight distinct retinal cell types.
Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.
Project description:Single cell RNA-sequencing has been applied to core and border regions of 9 colorectal tumors as well as to matched adjacent non-malignant colon tissue for the purpose of generating a cellular map of colorectal tumors and their tumor microenvironment.
Project description:Understanding dynamics of antigen specific B cell responses and link between BCR and B cell differentiation is crucial for our ability to direct immune responses and to generate memory and plasma cells responses to protective targets. Here we have infected mice with IAV-PR8 and sacrificed them at different days after infection (7-14-28). 2 naive mice were used as controls (spleen and lungs). From individual spleen, lungs and mediastinal lymph nodes we have sorted Hemagglutinin (HA)-specific IgD- B cells and single cell sequenced RNA and BCR. We identify several known and novel B cell subpopulations forming after infection and find organ-specific difference that persist over the course of the response. We found important transcriptional differences between memory cells in lungs and immune organs and describe organ-restricted clonal expansion. Strikingly, by combining BCR mutational analysis, monoclonal antibody expression and affinity measurements we found no differences between germinal center (GC)-derived memory and plasma cells, at odds with an affinity-based selection model. These finding provide the most comprehensive picture to date of organ specific antiviral B cell responses, differentiation, clonal-proliferation and dynamics.
Project description:Single-cell RNA sequencing of 697 YFP+ CD64+ lamina propria macrophages isolated from Cx3cr1CreERT2.Rosa26-LSL-YFP mice 35 weeks after tamoxifen administration
Project description:Heterogeneity of lung tumor endothelial cell (TEC) phenotypes across patients, species (human/mouse) and models (in vivo/vitro) remains poorly inventoried at the single-cell-level. We single-cell RNA-sequenced 56,771 ECs from human/mouse (peri)-tumoral lung and cultured human lung TECs, detected 17 known and discovered 16 novel phenotypes, including TECs presumably regulating immune surveillance. We resolved the canonical tip TECs into a known migratory tip and a novel basement-membrane remodeling breach phenotype. Tip-TEC signatures correlated with patient-survival, and tip/breach TECs were most sensitive to VEGF-blockade. By similarity analysis, only tip-TECs were congruent across species/models and shared conserved markers. Integrated analysis of the scRNA-seq data with orthogonal multi-omics and meta-analysis data across different human tumors, validated by functional analysis, identified collagen-modification as angiogenic candidate pathway.
Project description:To associate gene expression profiles with specific features of the splenic CD4+ T-cell repertoire generated during a blood stage P. chabaudi infection, we obtained both transcriptomic and T-cell receptor data from 2 infected mice at 7 days following infection.