Virus Dataset Detail

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Dataset Information
Accession GSE154386
Status 2021/1/1
Title Temporally integrated single cell RNA sequencing analysis of controlled and natural DENV-1 infections
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Controlled dengue human challenge studies present a unique opportunity to address many longstanding questions in the field of flavivirus biology. These fundamental questions include defining the early immunological signatures of infection, the host/environmental factors that impact disease severity, and the role of preexisting immunity on the development of symptomatic viral infection. However, while several controlled dengue human challenge studies have been performed and appear to clinically recapitulate may features of mild natural DENV infection, limited data are available on how the immunological and transcriptional response elicited by these attenuated challenge viruses compares to the profile associated with a natural, unattenuated DENV infection. To bridge this knowledge gap, we performed scRNAseq analysis on longitudinally collected PBMC samples obtained from 3 individuals (8 time points per subject) enrolled in the SUNY/WRAIR DENV-1 controlled human challenge study. In addition, 3 time points (two acute infection time points, one control time point) from two individuals experiencing a natural DENV-1 infection were analyzed and computationally integrated with the challenge model dataset. This temporally integrated dataset contains a total of 171,208 cells and 22 statistically distinct populations corresponding to all major anticipated leukocyte subsets. While all identified cell populations demonstrated significant and consistant perturbations in their transcriptional profile in response to either natural or experimental DENV infection, conventional monocytes respond most robustly to infection across all subjects and study groups from an unbiased transcriptional perspective. Using these data, core sets of genes that were consistently induced by either natural or experimental DENV were identified, and the overlap between the two arms of the study assessed.
Samples
GSM ID Sample info Characteristics Description
GSM4670192 Subject2_D0 cell type:PBMC; subject:DHIM_Subject2; study day:0 -
GSM4670193 Subject2_D2 cell type:PBMC; subject:DHIM_Subject2; study day:2 -
GSM4670194 Subject2_D4 cell type:PBMC; subject:DHIM_Subject2; study day:4 -
GSM4670195 Subject2_D6 cell type:PBMC; subject:DHIM_Subject2; study day:6 -
GSM4670196 Subject2_D8 cell type:PBMC; subject:DHIM_Subject2; study day:8 -
GSM4670197 Subject2_D10 cell type:PBMC; subject:DHIM_Subject2; study day:10 -
GSM4670198 Subject2_D15 cell type:PBMC; subject:DHIM_Subject2; study day:15 -
GSM4670199 Subject2_D28 cell type:PBMC; subject:DHIM_Subject2; study day:28 -
GSM4670200 Subject3_D0 cell type:PBMC; subject:DHIM_Subject3; study day:0 -
GSM4670201 Subject3_D2 cell type:PBMC; subject:DHIM_Subject3; study day:2 -
GSM4670202 Subject3_D4 cell type:PBMC; subject:DHIM_Subject3; study day:4 -
GSM4670203 Subject3_D6 cell type:PBMC; subject:DHIM_Subject3; study day:6 -
GSM4670204 Subject3_D8 cell type:PBMC; subject:DHIM_Subject3; study day:8 -
GSM4670205 Subject3_D10 cell type:PBMC; subject:DHIM_Subject3; study day:10 -
GSM4670206 Subject3_D14 cell type:PBMC; subject:DHIM_Subject3; study day:14 -
GSM4670207 Subject3_D28 cell type:PBMC; subject:DHIM_Subject3; study day:28 -
GSM4670208 Subject5_D0 cell type:PBMC; subject:DHIM_Subject5; study day:0 -
GSM4670209 Subject5_D2 cell type:PBMC; subject:DHIM_Subject5; study day:2 -
GSM4670210 Subject5_D4 cell type:PBMC; subject:DHIM_Subject5; study day:4 -
GSM4670211 Subject5_D6 cell type:PBMC; subject:DHIM_Subject5; study day:6 -
GSM4670212 Subject5_D8 cell type:PBMC; subject:DHIM_Subject5; study day:8 -
GSM4670213 Subject5_D10 cell type:PBMC; subject:DHIM_Subject5; study day:10 -
GSM4670214 Subject5_D14 cell type:PBMC; subject:DHIM_Subject5; study day:14 -
GSM4670215 Subject5_D28 cell type:PBMC; subject:DHIM_Subject5; study day:28 -
GSM4670216 Natural1_Dneg3 cell type:PBMC; subject:Natual_DENV_1; study day:-3 -
GSM4670217 Natural1_Dneg2 cell type:PBMC; subject:Natual_DENV_1; study day:-2 -
GSM4670218 Natural1_D180 cell type:PBMC; subject:Natual_DENV_1; study day:180 -
GSM4670219 Natural2_Dneg5 cell type:PBMC; subject:Natual_DENV_2; study day:-5 -
GSM4670220 Natural2_Dneg4 cell type:PBMC; subject:Natual_DENV_2; study day:-4 -
GSM4670221 Natural2_D180 cell type:PBMC; subject:Natual_DENV_2; study day:180 -
Platform GPL24676  : Illumina NovaSeq 6000 (Homo sapiens)
Literature 33513191  
Download Download scRNA Analysis Data  
scRNA-seq UMAP