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Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection [gene expression]

UID: 10821

Description
Summary from the GEO: " The relationship of SARS-CoV-2 lung infection and severity of pulmonary disease is not fully understood. We analyzed specimens from 24 autopsies from patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter- and intra- patient heterogeneity of pulmonary virus infection. There was a spectrum of high and low virus cases that was associated with duration of disease and activation of interferon pathway genes. Using a digital spatial profiling platform, the intra-pulmonary spatial heterogeneity of the virus corresponded to focal expression of interferon response genes and association with immune checkpoint genes
In this dataset, we capture the GeoMx DSP RNA profiling work done in conjunction with this study. The files here represent SARS-CoV-2 infected rapid autopsy patients (n = 6) which were profiled with the NanoString GeoMx COVID19 Atlas RNA panel v1.0. This panel was then read out using Illumina sequencing following standard library preparation according to manufacturer protocols. Attached below are low-resolution images of each slide with placement of all ROIs, as well as individual images of each ROI, segments, and UV illuminated IF channels."

Overall design from the GEO: "This dataset contains expression from localized sampling within 6 SARS-CoV-2 infected patient FFPE samples collected during rapid autopsy, with 3 non-infected control samples. Up to 48 segments were collected within each patient sample. RNA Scope on serial sections was used to guide ROI selection, and ROI ISH staining by RNA Scope is noted in the sample annotations."
Subject of Study
Homo sapiens
Severe acute respiratory syndrome coronavirus 2
Subject(s)
COVID-19
Immune Checkpoint Proteins
Interferons
SARS-CoV-2
Access via GEO

Plain text files of expression profiling by high throughput sequencing and compressed images
Accession #: GSE159787

Access via SRA

Transcriptome sequencing of 363 samples
Accession #: SRP292504

Access via BioProject

Additional information about the overall inititative.
Accession #: PRJNA678298

Access Restrictions
Free to All
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 NextSeq 550

Sequencing and array capabilities for transcriptome, targeted resequencing and genotype sequencing

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, TAR, gzip
Data Tool(s)
RNA Seq
Dataset Size
9.2 Mb (TAR), 406.7 Mb (ZIP), 42 Mb (TXT), 100+Gb (SRA)
Data Catalog Record Updated
2023-12-07