Gene Expression Nebulas

PRJNA631753

BioProject PRJNA631753
Project Name Spectrum of Viral Load and Host Response Seen in Autopsies of SARS-CoV-2 Infected Lungs
Species Homo sapiens
Tissue Bowel,Fat,Heart,Jejunum,Kidney,Liver,Lung,Marrow,Skin
Disease SARS-CoV-2 infection
Summary The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We visualized viral RNA by in situ hybridization and assessed the immune infiltrate using immunohistochemistry and total RNA sequencing on five COVID-19 positive patients. Patients with high levels of viral RNA showed hyaline membranes on histology, extensive pneumocyte loss, low T-cell numbers and were enriched for the interferon gene signature, while patients with lower levels of viral RNA showed lower numbers of T-cells and CD8 cells and were enriched for fibrosis-associated genes. The study highlights the need to assess both pulmonary viral load and immune response in patients with severe COVID-19 infection.
Overall Design Autopsy samples from patients deceased due to SARS-Cov2 infection were collected for total RNA-seq analysis to assess viral load and immune response.
Protocol
  • Growth Protocol: Rapid autopsy was performed for samples collection.
  • Treatment Protocol: -
  • Extract Protocol: RNA extraction from FFPE slides was done using the FormaPure Total nucleic acid extraction kit (C16675, Beckman Coulter) according to manufacturer instructions. Three 5 um thin tissue sections from areas devoid of acute inflammation were used per sample
  • Library Construction Protocol: The Smarter Stranded Total RNA-Seq kit v2 (634413, Illumina) was used with 10 ng RNA input, according to the manufacturer instructions to generate libraries.
Sequencing
  • Molecule Type: polyA RNA
  • Library Source:
  • Library Layout: PAIRED
  • Library Strand: Forward; -
  • Platform: ILLUMINA
  • Instrument Model: Illumina NextSeq 500
  • Strand-Specific: Specific; Unspecific

GEN Sample

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Analysis:
Data Resource 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 / Control 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

Bulk Expression Profiles

Gene Name Gene Accession Condition BioProject ID Sample Biological Condition Raw Counts FPKM TPM Editing Box Plot
Cell Type Cell Line Tissue Disease Disease State Development Stage