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Series GSE56192 Query DataSets for GSE56192
Status Public on Jun 10, 2014
Title Transcriptomic analysis of the Novel Middle East Respiratory Syndrome Coronavirus (Human, MRC5 cells)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We will use the EMC/2012 strain of the novel beta Coronavirus called Middle East Respiratory Syndrome Coronavirus (MERS-CoV). It was initially passaged on Vero E6 cells in Saudi Arabia before being sequenced at the Erasmus Medical College in Rotterdam, Netherlands by Dr Ron Fouchier. We propose to perform a time course of infection of hCoV-EMC on MRC5 cells (Human Lung origin) and Vero cells (African Green Monkey Kidney cells). Both cell lines readily grow and replicate the virus. Importantly these cell lines show signs of Cytopathic effect (CPE), such as cell rounding and release from the petri dish that coincide with time points high virus replication demonstrating the effects of virus replication on the cells. Transcriptomic analysis will be performed after infection with MERS-CoV and SARS-CoV (Urbani strain) to compare the host gene induction that occurs during infection.
Overall design MRC5 and Vero E6 cells will be infected at an MOI of 0.1 and 3 and RNA harvested from cells at 24 and 48 post infection. RNA will be processed for library creation and sequenced on an Illumina Hiseq. Sequencing reads will be analyzed and compared across the time course and between each virus to identify common response pathways induced during infection as well as unique pathways specific to each virus.
Contributor(s) Frieman M, Coleman C, Daugherty SC, Rasko D, Shefchek K, Sengamalay N, Tallon LJ, Sadzewicz L, Fraser CM
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BioProject PRJNA233943
Submission date Mar 26, 2014
Last update date May 15, 2019
Contact name David A Rasko
Phone 410 706 6774
Organization name University of Maryland School of Medicine
Department Istitute for Genome Sciences/Microbiology and Immunology
Street address 801 W. Baltimore Street, Room 619
City Baltimore
State/province MD
ZIP/Postal code 21201
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (37)
GSM1387907 MOCK_MRC5_1
GSM1387908 MOCK_MRC5_2
GSM1387909 MOCK_MRC5_3
This SubSeries is part of SuperSeries:
GSE56189 Transcriptomic Analysis Of The Novel Middle East Respiratory Syndrome Coronavirus (MERS-CoV)
SRA SRP040070

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Supplementary file Size Download File type/resource
GSE56192_RAW.tar 57.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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