Accession	GSE130891
Status	2019/5/9
Title	MeRIP-seq for host response to Flaviviridae infection
Organism	Homo sapiens
Experiment type	Expression profiling by high throughput sequencing;Other
Summary	The modification N6-methyladenosine (m6A) affects rates of translation and degradation of mRNA transcripts. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV) using MeRIP-seq. We used the uninfected replicates, among which we would expect little biological variation in methylation, as negative controls to validate statistical methods for the detection of m6A changes in MeRIP-seq data. Applying validated statistical methods, we found that innate immune response to Flaviviridae viruses alters m6A modification of specific cellular transcripts compared to uninfected controls. Finally, we find that these changes in m6A can in turn affect splicing or translation of genes relevant to infection.
Samples	GSM ID Sample info Characteristics Description GSM3755800 denv_48h_1_Input cell line:Huh7; viral strain:DENV2-NGC; library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;denv_48h_1.macs2_peaks.narrowPeak GSM3755801 denv_48h_1_IP cell line:Huh7; viral strain:DENV2-NGC; library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;denv_48h_1.macs2_peaks.narrowPeak GSM3755802 denv_48h_2_Input cell line:Huh7; viral strain:DENV2-NGC; library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;denv_48h_2.macs2_peaks.narrowPeak GSM3755803 denv_48h_2_IP cell line:Huh7; viral strain:DENV2-NGC; library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;denv_48h_2.macs2_peaks.narrowPeak GSM3755804 denv_48h_3_Input cell line:Huh7; viral strain:DENV2-NGC; library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;denv_48h_3.macs2_peaks.narrowPeak GSM3755805 denv_48h_3_IP cell line:Huh7; viral strain:DENV2-NGC; library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;denv_48h_3.macs2_peaks.narrowPeak GSM3755806 hcv_48h_1_Input cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;hcv_48h_1.macs2_peaks.narrowPeak GSM3755807 hcv_48h_1_IP cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;hcv_48h_1.macs2_peaks.narrowPeak GSM3755808 hcv_48h_2_Input cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;hcv_48h_2.macs2_peaks.narrowPeak GSM3755809 hcv_48h_2_IP cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;hcv_48h_2.macs2_peaks.narrowPeak GSM3755810 hcv_48h_3_Input cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;hcv_48h_3.macs2_peaks.narrowPeak GSM3755811 hcv_48h_3_IP cell line:Huh7; viral strain:HCV genotype 2A JFH-1 (culture adapted); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;hcv_48h_3.macs2_peaks.narrowPeak GSM3755812 wnv_48h_1_Input cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;wnv_48h_1.macs2_peaks.narrowPeak GSM3755813 wnv_48h_1_IP cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;wnv_48h_1.macs2_peaks.narrowPeak GSM3755814 wnv_48h_2_Input cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;wnv_48h_2.macs2_peaks.narrowPeak GSM3755815 wnv_48h_2_IP cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;wnv_48h_2.macs2_peaks.narrowPeak GSM3755816 wnv_48h_3_Input cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;wnv_48h_3.macs2_peaks.narrowPeak GSM3755817 wnv_48h_3_IP cell line:Huh7; viral strain:WNV-NY2000 (3000.0259); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;wnv_48h_3.macs2_peaks.narrowPeak GSM3755818 zikv_48h_1_Input cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;zikv_48h_1.macs2_peaks.narrowPeak GSM3755819 zikv_48h_1_IP cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;zikv_48h_1.macs2_peaks.narrowPeak GSM3755820 zikv_48h_2_Input cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;zikv_48h_2.macs2_peaks.narrowPeak GSM3755821 zikv_48h_2_IP cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;zikv_48h_2.macs2_peaks.narrowPeak GSM3755822 zikv_48h_3_Input cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:RNA-seq; time point:48 hours; treatment:infected; antibody:none processed data file:;zikv_48h_3.macs2_peaks.narrowPeak GSM3755823 zikv_48h_3_IP cell line:Huh7; viral strain:ZIKV-PR2015 (PRVABC59); library strategy:MeRIP-seq; time point:48 hours; treatment:infected; antibody:NEB anti-m6A antibody processed data file:;zikv_48h_3.macs2_peaks.narrowPeak GSM3755824 mockH_48h_1_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockH_48h_1.macs2_peaks.narrowPeak GSM3755825 mockH_48h_1_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_48h_1.macs2_peaks.narrowPeak GSM3755826 mockH_48h_2_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockH_48h_2.macs2_peaks.narrowPeak GSM3755827 mockH_48h_2_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_48h_2.macs2_peaks.narrowPeak GSM3755828 mockH_48h_3_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockH_48h_3.macs2_peaks.narrowPeak GSM3755829 mockH_48h_3_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_48h_3.macs2_peaks.narrowPeak GSM3755830 mockL_48h_1_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockL_48h_1.macs2_peaks.narrowPeak GSM3755831 mockL_48h_1_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_48h_1.macs2_peaks.narrowPeak GSM3755836 mockH_24h_1_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:24 hours; treatment:uninfected; antibody:none processed data file:;mockH_24h_1.macs2_peaks.narrowPeak GSM3755832 mockL_48h_2_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockL_48h_2.macs2_peaks.narrowPeak GSM3755833 mockL_48h_2_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_48h_2.macs2_peaks.narrowPeak GSM3755837 mockH_24h_1_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:24 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_24h_1.macs2_peaks.narrowPeak GSM3755834 mockL_48h_3_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:48 hours; treatment:uninfected; antibody:none processed data file:;mockL_48h_3.macs2_peaks.narrowPeak GSM3755835 mockL_48h_3_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:48 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_48h_3.macs2_peaks.narrowPeak GSM3755838 mockH_24h_2_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:24 hours; treatment:uninfected; antibody:none processed data file:;mockH_24h_2.macs2_peaks.narrowPeak GSM3755839 mockH_24h_2_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:24 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_24h_2.macs2_peaks.narrowPeak GSM3755840 mockH_24h_3_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:24 hours; treatment:uninfected; antibody:none processed data file:;mockH_24h_3.macs2_peaks.narrowPeak GSM3755841 mockH_24h_3_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:24 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockH_24h_3.macs2_peaks.narrowPeak GSM3755842 mockL_16h_1_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:16 hours; treatment:uninfected; antibody:none processed data file:;mockL_16h_1.macs2_peaks.narrowPeak GSM3755843 mockL_16h_1_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:16 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_16h_1.macs2_peaks.narrowPeak GSM3755844 mockL_16h_2_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:16 hours; treatment:uninfected; antibody:none processed data file:;mockL_16h_2.macs2_peaks.narrowPeak GSM3755845 mockL_16h_2_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:16 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_16h_2.macs2_peaks.narrowPeak GSM3755846 mockL_16h_3_Input cell line:Huh7; viral strain:none; library strategy:RNA-seq; time point:16 hours; treatment:uninfected; antibody:none processed data file:;mockL_16h_3.macs2_peaks.narrowPeak GSM3755847 mockL_16h_3_IP cell line:Huh7; viral strain:none; library strategy:MeRIP-seq; time point:16 hours; treatment:uninfected; antibody:NEB anti-m6A antibody processed data file:;mockL_16h_3.macs2_peaks.narrowPeak
Platform	GPL16791  : Illumina HiSeq 2500 (Homo sapiens)
Literature	31810760  32313079