Gene Expression
Nebulas
Gene Expression NebulasSummary: In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on 77 peripheral blood samples across 46 subjects with COVID-19 and compared them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. The transcriptome in peripheral blood reveals unique aspects of the immune response in COVID-19 and provides for novel biomarker-based approaches to diagnosis.
Overall Design: To define the host peripheral blood transcriptional response in subjects with SARS-CoV-2 infection, we performed RNA sequencing on samples from 46 individuals with PCR-positive, symptomatic SARS-CoV-2 infection, 14 of which were sampled at multiple timepoints. Subjects were enrolled when they presented for clinical care, and the time from symptom onset was recorded for each individual sample collected (range 1-35 days). Subjects with COVID-19 were divided based on disease severity and time from symptom onset (early <=10 days, middle 11-21 days, late >21 days). As comparators, we profiled banked blood samples from patients presenting to the Emergency Department with acute respiratory infection (ARI) due to seasonal coronavirus (n=59), influenza (n=17 or bacterial pneumonia (n=20), and matched healthy controls (n=19).
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| Extract Protocol: | Total RNA was extracted from peripheral blood preserved in PAXgene Blood RNA tubes using QIAGEN PAXgene miRNA Extraction Kit according to manufacturer's instructions. |
| Library Construction Protocol: | Libraries were prepared using NUGEN Universal Plus mRNA-seq with AnyDeplete Globin Kit according to manufacturer's instructions. |
| Molecule Type: | Poly(A)+ RNA |
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| Library Layout: | PAIRED |
| Library Strand: | Reverse |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina NovaSeq 6000 |
| Strand-Specific: | Specific |
| 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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