Search Tips
Description
Summary from the GEO: "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 from the GEO: "Autopsy samples from patients deceased due to SARS-Cov2 infection were collected for total RNA-seq analysis to assess viral load and immune response."
Subject of Study
Homo sapiens
Subject(s)
Alveolar Epithelial Cells
COVID-19
Hyalin
SARS-CoV-2
T-Lymphocytes
Viral Load
Access via GEO

Plain text files of expression profiling by high throughput sequencing
Accession #: GSE150316

Access via SRA

RNA sequencing of 88 samples.
Accession #: SRP261138

Access via BioProject

Additional information about the overall inititative.
Accession #: PRJNA631753

Access Instructions
The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files. The SRA Run Selector link at the bottom of the page is a processing tool for raw data.
Associated Publications
Desai N, Neyaz A, Szabolcs A, et al. Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection. Nature Communications. 2020; 11:6319.
Data Type
Genomic
Equipment Used
Illumina MiSeq

The MiSeq is an integrated instrument that performs clonal amplification, genomic DNA sequencing, and data analysis with base calling, alignment, variant calling, and reporting in a single run.

Nextseq 500 System

Whole Genome Sequencing System

Software Used
SRA Toolkit

The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.

Dataset Format(s)
Plain Text, SRA
Data Tool(s)
RNA Seq
Dataset Size
36.5 MB (TXT), 33.55 GB (SRA)
Data Catalog Record Updated
2023-12-07