Gene Expression
Nebulas
Gene Expression NebulasSummary: Severe COVID-19 may progress into acute respiratory distress syndrome (ARDS) with high mortality risk. Its exact pathological mechanism, therapeutic obstacles and the clinical sequelae are critical and unresolved issues. Here, we reported a representative COVID-19 induced ARDS case experienced initially stable, then suddenly deteriorating up to final respiratory failure courses, until his death despite of lung transplantation. His lung pathology showed necrosis of parenchymal tissues, extensive immune cell infiltration and lung fibrosis. Single-cell RNA sequencing revealed various immune cell populations were largely expanded in his lung, and manifested inflammatory/activated functions. We also showed that cell-crosstalk between lung macrophages and fibroblasts promoted pulmonary fibrosis through IL-1B and TGF-Β signaling pathways. Although SARS-CoV-2 RNA remained undetectable in his respiratory tract specimens including BALF at the later stage of his disease, the presence of SARS-CoV-2 was definitely confirmed in his lung tissues. Thus, this case indicates the pathological mechanism of severe COVID-19 includes pulmonary SARS-CoV-2 persistence, deranged inflammation and the extensive lung fibrosis which set the barriers for effective treatments and indicate potential health complications for severe COVID-19 patients
Overall Design: Using 10x genomics to measure single-cell RNA sequence (scRNA-seq) to comprehensively characterize the lung microenvironment in 4 lung tissues from the same COVID-19 severe patient
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| Extract Protocol: | The scRNA-Seq libraries were prepared with Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics; PN-1000075, PN-1000073 and PN-120262) following the user guide provided. Briefly, Gel bead in Emulsion (GEM) are generated by combining barcoded Gel Beads, a Master Mix containing 20,000 cells, and Partitioning Oil onto Chromium Chip B. Reverse transcription (RT) takes place inside each GEM, after which cDNAs are pooled for amplification and library construction in bulk. Finished library molecules consist of Illumina adapters and sample indices, allowing pooling and sequencing of multiple libraries on a next-generation short read sequencer. |
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| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
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| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6000 |
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| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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