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Series GSE125241 Query DataSets for GSE125241
Status Public on Jan 17, 2019
Title West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary West Nile virus (WNV) is a neurotropic mosquito-borne flavivirus of global importance. Neuroinvasive WNV infection results in encephalitis and can lead to prolonged neurological impairment or death. Type I interferon (IFN-I) is crucial for promoting antiviral defenses through the induction of antiviral effectors, which function to restrict viral replication and spread. However, our understanding of the antiviral response to WNV infection is mostly derived from analysis of bulk cell populations. It is becoming increasingly apparent that substantial heterogeneity in cellular processes exists among individual cells, even within a seemingly homogenous cell population. Here, we present WNV-inclusive single-cell RNA sequencing (scRNA-seq), an approach to examine the transcriptional variation and viral RNA burden across single cells. We observed that only a few cells within the bulk population displayed robust transcription of IFN-β mRNA, and this did not appear to depend on viral RNA abundance within the same cell. Furthermore, we observed considerable transcriptional heterogeneity in the IFN-I response, with genes displaying high unimodal and bimodal expression patterns. Broadly, IFN-stimulated genes negatively correlated with viral RNA abundance, corresponding with a precipitous decline in expression in cells with high viral RNA levels. Altogether, we demonstrated the feasibility and utility of WNV-inclusive scRNA-seq as a high-throughput technique for single-cell transcriptomics and WNV RNA detection. This approach can be implemented in other models to provide insights into the cellular features of protective immunity and identify novel therapeutic targets.
Overall design Bulk RNA sequencing and WNV-inclusive single-cell RNA sequencing were performed for WNV-infected L929 cells with and without reduced in vitro spread
Contributor(s) O’Neal JT, Upadhyay AA, Wolabaugh A, Patel NB, Bosinger SE, Suthara MS, Tharp GK
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Submission date Jan 17, 2019
Last update date Feb 11, 2019
Contact name Gregory K Tharp
Phone 404-727-7797
Organization name Yerkes National Primate Research Center
Department Developmental and Cognitive Neuroscience
Lab Genomics Core
Street address 954 Gatewood Dr
City Atlanta
State/province GA
ZIP/Postal code 30329-4208
Country USA
Platforms (1)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (136)
GSM3567001 SingleCell_WNV Infected_1
GSM3567002 SingleCell_WNV Infected_10
GSM3567003 SingleCell_WNV Infected_11
BioProject PRJNA515627
SRA SRP179956

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Supplementary file Size Download File type/resource
GSE125241_STAR_log2cpm_qc_withWNV.txt.gz 7.2 Mb (ftp)(http) TXT
GSE125241_allnormalized_deseq_counts+1.txt.gz 894.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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