Dataset - Omics, Proteomics, Transcriptomics, Microarray Systems Virology Lethal Human Virus, SARS-CoV Experiment SCL005

https://doi.org/10.25584/LHVSCL005/1661964
Biology
Human Health
Virus
Viruses
Virology
Health

 

Systems Virology Lethal Human Virus, SARS-CoV Experiment SCL005

New uploads pending

The purpose of this experiment was to evaluate the human host response to wild type virus icSARS-CoV Urbani and mutant virus icSARS deltaORF6 (DORF6) infection for subsequent transcriptional and proteomic analysis in human lung cell lines (2B4, clonal derivative of human lung Calu-3 cells) with high ACE2 expression.

2B-4 cells are a clonal population of Calu-3 cells sorted for high levels of expression of the SARS-CoV cellular receptor, angiotensin converting enzyme 2 (ACE2). 

 

Host Factor Experimental Design

  • Organism: Homo sapiens
  • Tissue Type: BTO:0001911 (lung)
  • Cell Lines: BTO:0002750 (Calu-3 2B4, human lung adenocarcinoma cell line)
  • Viral Pathogen: SARS coronavirus Urbani and infectious clone (ic) recombinant virus icSARS strains of SARS-CoV
  • Viral Subtypes: WT icSARS CoV Urbani and mutant icSARS-CoV ΔORF6 (deltaORF6)
  • Collection Attribute: Time course
  • Time Course: 0, 3, 7, 12, 24, 30, 36, 48, 54, 60, 72 hrs post infection. Time matched mocks were performed for both RNA and protein, in triplicate (n=3), defined as 3 different wells plated at the same time using the same cell stock for all replicates.
  • Treatment: 5 MOI; inoculation medium for mock infection was the same as the medium used for virus infection.

 

Data Available at Download Button:

Dataset downloads contain one or more statistically processed data file related to a lipidomic, transcriptomic, metabolomic, and/or proteomic dataset collection associated with the SARS experimental study.

 

Transcriptomics

Expression profiling by array (mRNA)

Proteomics 

Liquid Chromatography-Mass Spectrometry (LC-MS)

 

Linked Experimental Data Metadata

NCBI BioProject:  PRJNA149059

GEO Accession: GSE33267 (Whole Human Genome Microarray)

PRIDE Accession: PRD000594 (19877–19890)

PeptideAtlas Accession: PASS00430

IRD Experiment ID(s): SCL005-R (transcriptome), SCL005-P (proteome)

ViPR/IRD Method DOI: 10.35083/MJPG-M062

GenBank Accession: SARS coronavirus Tor2  | AY278741

Viral Taxon: 227984

 

Raw Data References:

  1. Sims AC, Tilton SC, Menachery VD, Gralinski LE, Schäfer A, Matzke MM, Webb-Robertson BJ, Chang J, Luna ML, Long CE, Shukla AK, Bankhead AR 3rd, Burkett SE, Zornetzer G, Tseng CT, Metz TO, Pickles R, McWeeney S, Smith RD, Katze MG, Waters KM, Baric RS. Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol. 2013 Apr;87(7):3885-902. doi: 10.1128/JVI.02520-12. Epub 2013 Jan 30. PMID: 23365422.
  2. Yount B, Roberts RS, Sims AC, Deming D, Frieman MB, Sparks J, Denison MR, Davis N, Baric RS. Severe acute respiratory syndrome coronavirus group-specific open reading frames encode nonessential functions for replication in cell cultures and mice. J Virol. 2005 Dec;79(23):14909-22. doi: 10.1128/JVI.79.23.14909-14922.2005. PMID: 16282490. 

 

English
Publications (4)
Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells
Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches To Control Interferon-Stimulated Gene Responses
Hypergraph models of biological networks to identify genes critical to pathogenic viral response
A comprehensive collection of systems biology data characterizing the host response to viral infection
People (3)
Lindsey N. Anderson

Lindsey Anderson’s research has been dedicated to the identification and characterization of novel, targeted and non-targeted, functional metabolic interactions using a high-throughput systems biology and computational biology approach. Her expertise in functional metabolism and multidisciplinary...

Jason McDermott

Dr. Jason McDermott, senior research scientist, has extensive research experience in molecular and structural virology and data resource design, data integration and prediction of biological networks, bridging experimental and computational biology. Currently, his research interests include data...

Katrina Waters

Dr. Katrina Waters is the division director for Biological Sciences at the Pacific Northwest National Laboratory. Waters has a Ph.D. in biochemistry and more than 15 years of experience in microarray and proteomics data analysis. Her research interests are focused on the integration of genomics...

Data Sources (2)
Q Exactive Plus Mass Spectrometer
Agilent Gene Expression Profiling Technologies