biostudies-arrayexpressAllison DupzykHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15272QIC-seq combines virus-inclusive and perturb single cell RNA sequencing in order to systematically compare host factor requirements among divergent flaviviruses.biostudies-arrayexpressSample Collection - After 48 hours of mock or infection, cells were washed, and trypsinized and resuspended in PBS and BSA to prevent clumping.Sequencing - Illumina NGS on Novaseq lane. PE150. Sequencing conducted by NovogeneGrowth Protocol - Cells were grown in complete DMEM or IMDM media supplemented with 10% FBS.Sample Treatment - Cells were either mock infected or infected with virus at varying MOIs for 48 hours.Nucleic Acid Extraction - Cells were lysed, and RT-PCR was used to capture host transcriptome, viral genomes, and sgRNAs to identify perturbed cells. cDNA was size selected to generate a larger cDNA library (transcriptomic) and a smaller DNA library (viral and CRISPR) .Library Construction - 10X genomics 5' VDJ protocol was followed for the transcriptomic library, READ2 was placed onto cDNA in small viral and CRISPR library by PCR before re-incorporation into the remaining protocol.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - 10X Genomics Cellranger was used.Data Transformation - Data was normalized using Seurat's SCTransformation or normalize data function().UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsHomo sapiensAllison DupzykfalseQIC-seq of Huh7.5.1 cells challenged with DENV, WNV, YFV, and LGTV. QIC-seq of Hap1 cells challenged with DENV and WNVQIC-seq combines virus-inclusive and perturb single cell RNA sequencing in order to systematically compare host factor requirements among divergent flaviviruses.2026-04-17T00:00:00Z2026-04-17T20:38:38.167Z2025-06-25T15:53:19.877ZE-MTAB-15272ERP174043EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969