Project description:Use of single-cell transcriptomics to test early HD selective vulnerability by comparing CTRL and HD telencephalic organoids at day 45 and 120 of differentiation. To test the influence and the interactions between healthy and HD cells, chimeric organoids composed of CTRL and HD cells juxtaposed within the same organoid were grown and analyzed by scRNAseq at day 120.
Project description:To further explore the transcriptional changes in the kidney transplant biopsy at time of rejection, scRNAseq analysis was performed on 16 kidney transplant biopsy-derived cells using 10X Genomic technology.
Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile 13-week post-conception distal human fetal lung explants cultured in an air liquid interface system and treated with an LGR5 ectodomain adenovirus that inhibits R-Spondin function or control adenovirus. A third, non-infected, condition was also sequenced. We also performed scRNA-seq on distal human fetal lung tissue from an 8.4-week post-conception biological specimen. Diverse cell lineages were captured in all data sets, and include epithelium, mesenchyme, immune, neurons, and endothelium.
Project description:This study contains single cell RNA-seq of the non-small cell lung cancer line HCC827 in three conditions. Firstly we have sequenced the RNA of single cells of a culture of HCC827 cells grown in normal conditions (POT). In our study we then evolved two arms of the cell line, one in the presence of the drug gefitinib (40nM, G1) and the other in the presence of trametinib (100nM, T4) in HYPERflasks to avoid replating. These data were analysed using cellRanger using GRCh38. Output from cellRanger was filtered for a minimum number of detected genes and UMIs. Mitochondrial reads were excluded from analysis (Acar_2020_single_cell_raw_data.txt). The data was then imported and scaled using the package Seurat. Scaled data was then filtered for low expression of housekeeping genes. Additionally genes expressed in fewer than 20 cells were excluded from analysis. Data was then renormalised using linear normalisation and scaling on the filtered raw data (Acar_2020_single_cell_processed_data.txt). Principal component analysis was run on variable genes identified using Seurat and the top 44 component were used as input for t-SNE analysis. Clusters were then identified using FindClusters in Seurat (Acar_2020_single_cell_metadata.txt). For a full description see the associated publication.
Project description:Here, we performed single-cell RNA sequencing (scRNA-seq) of a human fetal jejunum tissue sample from 1 individual biological specimen age 40 weeks post conception. The data set is composed of cells from diverse intestinal lineages.
Project description:Here, we performed single cell RNA sequencing (scRNA-seq) of human fetal ileum tissue samples from 3 individual biological specimens ages 11.4, 14.4, and 18.9 weeks post conception. The data set is composed of over 16,000 cells from diverse intestinal lineages.
Project description:In this study, we analysed early embryonic skin development (mus musculus; C57BL/6J) at the transcriptional level. Major questions concerned the cell type composition of early embryonic skin, and the emergence of transcriptional heterogeneity among epithelial and stromal precursor cells. Cells were isolated from embryonic dorsal skin and randomly sequenced (scRNA-Seq using 10X Genomics v2) without any cell sorting. Data from three embryonic time points (E12.5, E13.5, and E14.5) was integrated and compared to obtain a better understanding of the dynamics of early skin development.
Project description:Longitudinal phenotyping of T cells and myeloid cells in early (day 14) and late (day26) GL261 tumors. Single cell RNA sequencing of CD45+ immune cell from intracranial murine GL261-SIINFEKL tumors 20 days after inoculation. SIINFEKL-reactive T cells were sorted based on dextramer staining. Using time-resolved scRNA-seq of murine tumor-infiltrating immune cells from early (d14) and late stage (d26) syngeneic GL261 gliomas we observed constant MHCII expression by murine microglia over time and overall high but decreasing MHCII expression in late stage bbm indicating a dynamic process of MHCII expression. We show that loss of major histocompatibility complex (MHC) class II (MHCII)-restricted antigen presentation on bbm drives dysfunctional intratumoral tumor-reactive CD8+ T cell states through increased expression of Tox, a critical regulator of T cell exhaustion. By calculating the normalized abundance of T cell states along the pseudotime trajectory of SIINFEKL-reactive CD8+ T cells retrieved from myeloidMHCII-proficient and -deficient microenvironments, we found an enrichment of a distinct T cell state in myeloidMHCIIKO CD8+ T cells that was defined by peak expression of exhaustion markers. Mechanistically, MHCII-dependent activation of CD4+ T cells restricts myeloid-derived osteopontin that triggers a chronic activation of nuclear factor of activated T cells (Nfat)2 in tumor-reactive CD8+ T cells. In summary, we provide evidence that MHCII-restricted antigen presentation on bbm is a key mechanism to directly maintain functional cytotoxic T cell states in brain tumors.
Project description:Angiogenesis-inhibitor (AI) drugs targeting vascular endothelial growth factor (VEGF) signalling to the endothelial cell (EC) are used to treat various cancers types. However, primary or secondary resistance to therapy is common. Clinical and pre-clinical studies suggest that other alternative pro-angiogenic factors are up-regulated after VEGF-pathway inhibition. Therefore, identification alternative pro-angiogenic pathway(s) is critical for the development of more effective anti-angiogenic therapy. Here we study the role of apelin as a pro-angiogenic G-protein coupled receptor (GPCR) ligand in tumor growth and angiogenesis. We applied single-cell RNA-sequencing to Mouse Lewis lung carcinoma (LLC1) or B16F10 mouse melanoma cell lines (1 X 106) implanted subcutaneously into the flanks of 12 weeks old Apln-/y or littermate control mice in combination with sunitinib or control (vehicle) treatment. We found apelin loss reduced angiogenic sprouting and tip cell marker gene expression in comparison to the sunitinib-alone treated mice and prevented EC tip cell differentiation.