biostudies-arrayexpressDan YuanHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-13745This study included single-cell RNA-seq and scATAC-seq data from PBMCs from 12 COVID-19 individuals at acute infectionbiostudies-arrayexpressNucleic Acid Extraction - Briefly, cryopreserved PBMCs were thawed in RPMI with 10% FBS and resuspended in 1X red blood cell lysis solution (Miltenyi Biotech) to lyse residual red blood cells. Neutrophils were depleted and B cells were enriched from PBMC samples using CD66b-biotin antibodies and the B cell enrichment kit (Miltenyi Biotech). Enriched B cells were lysed in Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin, 1% BSA, 1 mM DTT and 1 U/μl RNase inhibitor in nuclease-free water) for three minutes on ice. Lysed nuclei were washed three times in Wash Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT and 1 U/μl RNase inhibitor in nuclease-free water) before loaded onto the Chromium Next GEM Chip J. Gene expression and ATAC libraries were prepared according to manufacturer’s guidelines and sequenced on Nextseq 2000 (Illumina).Sample Collection - Briefly, cryopreserved PBMCs were thawed in RPMI with 10% FBS and resuspended in 1X red blood cell lysis solution (Miltenyi Biotech) to lyse residual red blood cells. Neutrophils were depleted and B cells were enriched from PBMC samples using CD66b-biotin antibodies and the B cell enrichment kit (Miltenyi Biotech). Enriched B cells were lysed in Lysis Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% digitonin, 1% BSA, 1 mM DTT and 1 U/μl RNase inhibitor in nuclease-free water) for three minutes on ice. Lysed nuclei were washed three times in Wash Buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 1 mM DTT and 1 U/μl RNase inhibitor in nuclease-free water) before loaded onto the Chromium Next GEM Chip J. Gene expression and ATAC libraries were prepared according to manufacturer’s guidelines and sequenced on Nextseq 2000 (Illumina).Sequencing - Libraries were sequenced on Nextseq 2000.---------------------------Library Construction - Libraries are constructed following instructions from 10X Genomics-------------------------MIAME ScoreOrganizationAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data are raw counts. They are not normalized. However, measures have been taken to remove low-quality cells, non-B cells and doublets.UnknownTranscriptomicsGenomicsProteomicsNextSeq 2000single nucleus RNA sequencingHomo sapiensDan YuanfalseSARS-CoV-2-induced transient atypical memory B cells are potent autoantibody-secreting precursorsThis study included single-cell RNA-seq and scATAC-seq data from PBMCs from 12 COVID-19 individuals at acute infection2025-04-26T00:00:00Z2024-01-29T22:17:36.963Z2024-01-29T22:17:36.963ZE-MTAB-13745EFO_0002944EFO_0004170EFO_0009809EFO_0005518EFO_0003816EFO_0004184