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Series GSE118305 Query DataSets for GSE118305
Status Public on Sep 10, 2018
Title Genome-wide RNA-seq and Epigenetic analysis of human monocyte derived macrophage responses to Zika virus infection
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Interpretation of genome-wide investigations of host-pathogen interactions are often obscured by analyses of mixed populations of infected and uninfected cells. Thus, we developed a system whereby we simultaneously characterize and compare genome-wide transcriptional and epigenetic changes in pure populations of virally-infected and neighboring uninfected cells to identify viral-regulated host-responses. Using patient-derived unmodified Zika viruses (ZIKV) infecting primary human macrophages, we reveal that ZIKV suppresses host transcription by multiple mechanisms. ZIKV infection causes both targeted suppression of type I interferon responses and general suppression by reducing RNA polymerase II protein levels and DNA occupancy. Simultaneous evaluation of transcriptomic and epigenetic features of infected and uninfected cells provide a powerful method for identifying coincident evolution of dominant pro-viral or anti-viral mechanisms.
 
Overall design Analysis of transcriptional and epigenetic response of human monocyte derived macrophages to Zika virus infection
 
Contributor(s) Carlin AF, Shresta S, Glass CK
Citation(s) 30206152
Submission date Aug 08, 2018
Last update date Mar 27, 2019
Contact name Aaron F Carlin
E-mail(s) acarlin@ucsd.edu
Organization name University of California, San Diego
Department Medicine
Lab Carlin
Street address 9500 Gilman Drive GPL Rm 108
City La Jolla
State/province California
ZIP/Postal code 92093-0651
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (60)
GSM3324430 Human1_RNA_Mock_24h
GSM3324431 Human1_RNA_FSS_ZIKVnegative_24h
GSM3324432 Human1_RNA_FSS_ZIKVpositive_24h
Relations
BioProject PRJNA485140
SRA SRP156762

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Supplementary file Size Download File type/resource
GSE118305_RAW.tar 6.5 Mb (http)(custom) TAR (of BED)
GSE118305_RNAseq_HMDM_ZIKV_2018.txt.gz 3.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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