E-PROT-77
Ontology highlight
ABSTRACT:
PROVIDER: E-PROT-77 | ExpressionAtlas | 2022-01-14
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Multiple distinct cell types of the human lung and airways have been defined by single cell RNA sequencing (scRNAseq). Here we present a multi-omics spatial lung atlas to define novel cell types which we map back into the macro- and micro-anatomical tissue context to define functional tissue microenvironments. Firstly, we have generated single cell and nuclei RNA sequencing, VDJ-sequencing and Visium Spatial Transcriptomics data sets from 5 different locations of the human lung and airways. Secondly, we define additional cell types/states, as well as spatially map novel and known human airway cell types, such as adult lung chondrocytes, submucosal gland (SMG) duct cells, distinct pericyte and smooth muscle subtypes, immune-recruiting fibroblasts, peribronchial and perichondrial fibroblasts, peripheral nerve associated fibroblasts and Schwann cells. Finally, we define a survival niche for IgA-secreting plasma cells at the SMG, comprising the newly defined epithelial SMG-Duct cells, and B and T lineage immune cells. Using our transcriptomic data for cell-cell interaction analysis, we propose a signalling circuit that establishes and supports this niche. Overall, we provide a transcriptional and spatial lung atlas with multiple novel cell types that allows for the study of specific tissue microenvironments such as the newly defined gland-associated lymphoid niche (GALN).
2022-01-06 | E-MTAB-11640 | biostudies-arrayexpress
Project description:Aging promotes lung function decline and susceptibility to chronic lung diseases, which are the third leading cause of death worldwide. We used single cell transcriptomics and mass spectrometry to quantify changes in cellular activity states of 30 cell types and the tissue proteome from lungs of young and old mice. Aging led to increased transcriptional noise, indicating deregulated epigenetic control. We observed highly distinct effects of aging on cell type level, uncovering increased cholesterol biosynthesis in type-2 pneumocytes and lipofibroblasts as a novel hallmark of lung aging. Proteomic profiling revealed extracellular matrix remodeling in old mice, including increased collagen IV and XVI and decreased Fraser syndrome complex proteins and Collagen XIV. Computational integration of the aging proteome and single cell transcriptomes predicted the cellular source of regulated proteins and created a first unbiased reference of the aging lung. The lung aging atlas can be accessed via an interactive user-friendly webtool at: https://theislab.github.io/LungAgingAtlas
2019-01-21 | PXD012307 | Pride
Project description:Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations.
2024-02-25 | GSE255460 | GEO
Project description:A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
2024-03-19 | E-PROT-29 | ExpressionAtlas
Project description:Arabidopsis proteomic tissue atlas
2023-12-19 | E-PROT-135 | ExpressionAtlas
Project description:Gene expression changes during ageing were shown to oppose developmental trajectories; a reversal pattern previously linked to cellular identity loss. Generating cortex, lung, liver and muscle tissue transcriptomes of 16 mice of different ages, covering development and ageing periods, we found that expression reversals were widespread but tissue-specific. Consistent with this result, we observed an inter-tissue divergence during development and convergence during ageing (DiCo), further confirmed in independent mouse and human datasets. The genes displaying DiCo pattern were enriched among tissue-specific genes that tended to lose developmental expression levels during ageing. Finally, analysing publicly available single-cell transcriptome data, we studied the contribution of cellular composition and cell-autonomous changes to the convergence in ageing. Our results, for the first time, suggest inter-tissue convergence during ageing is widespread and associated with the loss of specialisation at the tissue and possibly also at the cellular level.
2022-02-02 | GSE167665 | GEO
Project description:mESC shotgun and positional proteomics based on deep proteome sequence database (derived from RIBOseq data)
2021-11-09 | E-PROT-17 | ExpressionAtlas
Project description:Single-cell transcriptomic atlas of leukocytes of biopsy fluid (n = 2), blood (n = 2) and CSF (n = 1), and spatial transcriptomics of biopsy tissue (n = 4) from primary CNS B cell lymphoma patients.
2022-08-23 | GSE203552 | GEO
Project description:Epigenetic atlas of ageing mouse heart
2022-12-01 | E-MTAB-8826 | biostudies-arrayexpress
Project description:Understanding the molecular and cellular processes involved in lung epithelial regeneration may fuel the development of therapeutic approaches for lung diseases. We combine mouse models allowing diphtheria toxin-mediated damage of specific epithelial cell types and parallel GFP-labeling of functionally dividing cells with single-cell transcriptomics to characterize the regeneration of the distal lung. We uncover cell types, including Krt13+ basal and Krt15+ club cells, detect an intermediate cell state between basal and goblet cells, reveal goblet cells as actively dividing progenitor cells, and provide evidence that adventitial fibroblasts act as supporting cells in epithelial regeneration. We also show that diphtheria toxin-expressing cells can persist in the lung, express specific inflammatory factors, and transcriptionally resemble a previously undescribed population in the lungs of COVID-19 patients. Our study provides a comprehensive single-cell atlas of the distal lung that characterizes early transcriptional and cellular responses to concise epithelial injury, encompassing proliferation, differentiation, and cell-to-cell interactions.
2024-01-19 | PXD039508 | Pride