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Series GSE89069 Query DataSets for GSE89069
Status Public on Oct 23, 2016
Title Next Generation Sequencing Facilitates Quantitative Analysis of brain Transcriptome after viral infection with ZIKV (Zika Virus)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The goals of this study are to understand ZIKV induced immune responses in the developing brain at genome-wide level.
Methods: Total RNA was isolated from E17.5 mouse brains after viral infection at E14.5. After genomic DNA and ribosomal RNA removal, fractionated RNA were subjected to strand-specific library preparation using NEBNext Ultra RNA Library Prep Kit. Sequencing was performed on Nextseq500 (Illumina). The sequencing reads that passed quality filters were analyzed with TopHat followed by Cufflinks.
Results: After performed Gene Ontology analyses with RNA-seq data, our results revealed a set of genes that are associated with the immune response and apoptosis pathways. Gene Set Enrichment Analysis (GSEA) further show significant enrichments on both the immune system response and apoptosis pathways. Some of these results were also verified with qRT-PCR.
Conclusions: Our results suggest that ZIKV infection triggers an aggressive immune response, which has the potential to cause exacerbation of brain damage by enhancing neuronal death and generating vascular abnormalities. Our discovery of massive neuronal death, leaky blood-brain-barrier (BBB), and astrogliosis in ZIKV infected brains is the first study to suggest that ZIKA causes extensive brain damage.
Overall design RNA-seq of C56BL/6 mouse E17.5 brain with or without Zika virus infection.
Contributor(s) Lai F, Chen J, Shao Q, Herrlinger S, Yang S, Moore JM, Brindley MA
Citation(s) 27729407
NIH grant(s)
Grant ID Grant title Affiliation Name
R00 HD073269 Wdr62 in neural development and malformations of cortical development disease UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC Chen
R01 NS096176 Genetic analysis of a microRNA pathway regulating neural tube closure UNIVERSITY OF GEORGIA RESEARCH FOUNDATION, INC Chen
Submission date Oct 22, 2016
Last update date May 15, 2019
Contact name Fan Lai
Phone 2154102111
Organization name University of Miami
Street address 1501 NW 10th Ave, BRB 731G
State/province FL
ZIP/Postal code 33136
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM2358319 Mock rep1
GSM2358320 Mock rep2
GSM2358321 ZIKV rep1
BioProject PRJNA350211
SRA SRP091952

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Supplementary file Size Download File type/resource
GSE89069_RAW.tar 5.0 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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