Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA401829 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The purpose of this experiment was to evaluate the human host cellular response to wild-type Human coronavirus strain 229E (HCoV-229E) infection of primary human airway epithelial cell cultures. Sample data was obtained from mock-infected primary human airway epithelial cell cultures at 24 hours post infection. Primary human conducting airway epithelial cells were grown at air-liquid interface. Samples were harvested and processed for RNA sequencing (RNA-Seq) expression analysis and limited proteolysis proteomics. Wild-type human coronavirus strain 229E (HCoV-229E) infected and mock-infected primary human airway epithelial cell cultures with and without primary human lung macrophages were harvested at 24 hour post infection (MOI 3). Samples were processed for RNA sequencing (RNA-Seq; in Trizol) expression analysis and limited proteolysis proteomics (LiP). For LiP, cells were lysed by freeze thaw cycles and each replicate was split in half and treated for 1 minute with proteinase K and then trypsin and the other half just treated with trypsin prior to processing for proteomic analysis. Search for the DDA data was performed using MaxQuant, following the label-free quantification and match between runs (LFQ-MBR) workflow. The DIA data was searched with FragPipe/DIA-NN. The database search results were further processed using in-house codes which filtered and normalized the data, and added statistical parameters.
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Project description:<p>Pulmonary fibrosis is a heterogenous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplification, these data provide a molecular atlas of disease pathobiology. We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to non-overlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. Analysis of a cryobiopsy specimen from a patient with early disease supports the clinical application of single-cell RNA-Seq to develop personalized approaches to therapy.</p>
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Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 16,015 nuclei in human adult testis. This dataset includes five samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
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