{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Justin Ooi"],"organism":["Homo sapiens"],"software":["Seurat V3"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16332"],"description":["Using a skin-blister induction model established for dengue, we investigated the transcriptional signatures and TCR repertoire of matched CD8 T cells in skin and blood samples"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted from skin blister fluids using the Pathogen 200 protocol on the Roche MagNA Pure 24 Instrument according to the manufacturer's instructions.","Library Construction - Sorted cells were mixed with 10x barcoded gel beads, loaded onto Chromium Next GEM Chip K and ran on the Chromium Controller X to generate GEMs. Post GEM-RT cleanup was then carried out, followed by cDNA amplification according to manufacturer’s protocol.  V(D)J amplification from cDNA, V(D)J, library construction as well as 5’ gene expression library construction were carried out according to manufacturer’s protocol.  Quality control was performed on the Agilent 2100 Bioanalyzer G2938C","Sample Collection - Whole blood was collected in K3EDTA tubes. PBMCs were isolated from whole blood by Ficoll-Paque gradient centrifugation.  Blisters were induced on the forearm of the patients using a clinical pump connected to a chamber. A negative pressure was applied until a blister was formed and the blister fluid was aspirated using a sterile needle. Skin cells were recovered by centrifugation at 3000 rpm for 10 minutes at 4°C.  CD8+ CD38+ HLA-DR+ cells from matched PBMCs and skin blister cells of dengue patients were sorted into AIM-V + 2% Human Serum on the BD FACSAria™ III Sorter following staining with antibodies targeting surface markers","Sequencing - Libraries were sequenced paired-end 150 base pairs on the Illumina HiSeq X System (20,000 read pairs per cell)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The filtered gene-barcode matrix of UMI counts was then analyzed with Seurat V3 for quality control, normalization, dimensional reduction, integration, clustering, and visualization."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["HiSeq X Ten"],"pubmed_abstract":["Dengue is spreading globally, and there is urgent need to define immune correlates of protection for this disease. Dengue infection first occurs in the skin following the bite of an infected mosquito; however, knowledge of host immune responses within this site remains sparse. We investigated the phenotypic, functional, and transcriptional profiles of skin and blood T cells in 73 patients with dengue and 10 healthy volunteers. We show that the skin T cell compartment undergoes marked reshaping and is strongly enriched with proliferating CD4<sup>+</sup> and CD8<sup>+</sup> T cells compared with the blood of patients. Activated skin CD8<sup>+</sup> T cells expressed a core transcriptional signature of tissue-resident memory T (T<sub>RM</sub>) cells, supporting their differentiation to the T<sub>RM</sub> cell lineage during infection. The magnitude of skin and blood CD8<sup>+</sup> T cell responses were associated with protection from hospitalization in this cohort. These data support a protective role of skin-resident and circulating CD8<sup>+</sup> T cells in dengue and warrant evaluation of vaccination strategies inducing skin T<sub>RM</sub> cells to enhance protective immunity."],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_title":["Dengue infection elicits skin tissue-resident and circulating CD8+ T-cells associated with protection from hospitalization"],"pubmed_authors":["Kuan Rong Chan","Noor Zayanah Hamis, Justin SG Ooi, Ka-Wai Cheung, Valerie Chew, Michaela Gregorova , Eugenia Ong Ziying, Kuan Rong Chan, Tun-Linn Thein, Yee-Sin Leo, David Chien Boon Lye, Eng Eong Ooi, Laura Rivino1","Laura Rivino","Justin Ooi"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNAseq and scTCRseq of human CD8 T cells from blood and skin compartments in Dengue patients","description":"Using a skin-blister induction model established for dengue, we investigated the transcriptional signatures and TCR repertoire of matched CD8 T cells in skin and blood samples","dates":{"release":"2026-04-14T00:00:00Z","modification":"2026-04-14T13:26:52.099Z","creation":"2025-12-03T18:04:45.044Z"},"accession":"E-MTAB-16332","cross_references":{"ENA":["ERP186112"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1126/sciadv.aea7987"]}}