biostudies-arrayexpressElie AntounHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14933We performed longitudinal analysis of three dominant SARS-CoV-2 spike-specific CD4+ T-cell responses carrying single-cell transcriptomic and TCR analysis from ex vivo tetramer+ cells from participants 1-3months post initial infection in 2020 and followed up at 3-4 years, with the aim to characterise the immunodominant CD4+ memory T cell responses 3-4 years post initial infection.biostudies-arrayexpressNucleic Acid Extraction - Single cells were directly sorted into 96-well PCR plates (Thermo Fisher Scientific) containing cell lysis buffer and stored at −80°C for further SmartSeq2 analysis.Sequencing - Sequencing was performed on Illumina NextSeq sequencing platform with NextSeq Control Software v.4, as single-end 72bp readsSample Collection - Patients were recruited from the John Radcliffe Hospital in Oxford, UK, between March 2020 and September 2021 by identification of patients hospitalized during the SARS-CoV-2 pandemic and recruited into the Sepsis Immunomics study. All patients were sampled at least 28 days after symptom onset during the primary infection, while 10 patients were further sampled around 3-4 years after initial infection.Library Construction - ScRNA-seq with ex vivo tetramer+ cells was performed using SmartSeq2 analysis as described previously (Picelli et al (2014)). Reverse-transcription (RT) and PCR amplification were performed with the exception of using ISPCR primer with biotin tagged at the 5′ end and increasing the number of cycles to 25. Sequencing libraries were prepared using the Nextera XT Library Preparation KitOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - BCL files were converted to FASTQ format using bcl2fastq v2.20.0.422 (Illumina). FASTQ files were aligned to human genome hg19 using STAR v2.6.1dData Transformation - Reads were counted using featureCounts (subread v2.0.0).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 550RNA-seq of coding RNA from single cellsHomo sapiensElie AntounfalseSmartSeq single-cell RNAseq of SARS-CoV-2 spike-specific CD4+ T cellsWe performed longitudinal analysis of three dominant SARS-CoV-2 spike-specific CD4+ T-cell responses carrying single-cell transcriptomic and TCR analysis from ex vivo tetramer+ cells from participants 1-3months post initial infection in 2020 and followed up at 3-4 years, with the aim to characterise the immunodominant CD4+ memory T cell responses 3-4 years post initial infection.2025-07-31T00:00:00Z2025-07-30T14:47:01.877Z2025-03-11T13:42:54.22ZE-MTAB-14933ERP170187EFO_0002944EFO_0004170EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184