{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Allison Dupzyk"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15272"],"description":["QIC-seq combines virus-inclusive and perturb single cell RNA sequencing in order to systematically compare host factor requirements among divergent flaviviruses."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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 Novogene","Growth 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - 10X Genomics Cellranger was used.","Data Transformation - Data was normalized using Seurat's SCTransformation or normalize data function()."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Allison Dupzyk"],"additional_accession":[]},"is_claimable":false,"name":"QIC-seq of Huh7.5.1 cells challenged with DENV, WNV, YFV, and LGTV. QIC-seq of Hap1 cells challenged with DENV and WNV","description":"QIC-seq combines virus-inclusive and perturb single cell RNA sequencing in order to systematically compare host factor requirements among divergent flaviviruses.","dates":{"release":"2026-04-17T00:00:00Z","modification":"2026-04-17T20:38:38.167Z","creation":"2025-06-25T15:53:19.877Z"},"accession":"E-MTAB-15272","cross_references":{"ENA":["ERP174043"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}