{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Eugenia Ong"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13441"],"description":["Single cell RNA-seq was conducted on peripheral blood mononuclear cells (PBMCs) collected from study participants that were dengue seronegative (n=3) or dengue seropositive (n=3). Baseline single cell gene expression profiling was conducted using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Blood was collected in EDTA tubes from subjects, and peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation with SepMate-50 tubes (Stemcell Technologies) according to manufacturer’s instructions.","Library Construction - Single cell library preparation was performed using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) by Molecular Genomics Pte Ltd. Profiles of cDNA samples and the final libraries were verified using Agilent High Sensitivity D5000 screentapes on an Agilent Tapestation 4200. At least 5000 cells were targeted per sample with at least 20,000 reads sequenced per cell.","Sequencing - Sequencing was performed using 2x150 paired-end (PE) chemistry on the Illumina Novaseq by Macrogen Inc.","Nucleic Acid Extraction - Frozen PBMCs were thawed and cells were counted using Nexcellom Cellometer Spectrum, and cell viability assessed using Live/DEAD Viability/Cytotoxicity Kit for mammalian cells (Thermo Scientific). Cells are then partitioned into nanoliter-scale gel beads-in-emulsion (GEMs). Gel beads are dissolved, primers are released and any co-partitioned cell is lysed. Incubation of GEMs generates barcoded, full length cDNA from poly-adenylated mRNA."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Eugenia Ong"],"data_protocol":["Data Transformation - The filtered gene-barcode matrix of UMI counts was then analyzed with Seurat V5 for quality control, normalization, dimensional reduction, integration, clustering, and visualization.","Sequence Alignment - Raw sequencing data was processed using the Cell Ranger pipeline (10x Genomics)."],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA-Seq of dengue seronegative and seropositive individuals","description":"Single cell RNA-seq was conducted on peripheral blood mononuclear cells (PBMCs) collected from study participants that were dengue seronegative (n=3) or dengue seropositive (n=3). Baseline single cell gene expression profiling was conducted using 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index).","dates":{"release":"2025-09-08T00:00:00Z","modification":"2025-09-09T00:02:07.702Z","creation":"2023-10-17T11:57:54.069Z"},"accession":"E-MTAB-13441","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}