{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dan Yuan"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13745"],"description":["This study included single-cell RNA-seq and scATAC-seq data from PBMCs from 12 COVID-19 individuals at acute infection"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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-------------------------"],"figure_sub":["MIAME Score","Organization","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Data are raw counts. They are not normalized. However, measures have been taken to remove low-quality cells, non-B cells and doublets."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["single nucleus RNA sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Dan Yuan"],"additional_accession":[]},"is_claimable":false,"name":"SARS-CoV-2-induced transient atypical memory B cells are potent autoantibody-secreting precursors","description":"This study included single-cell RNA-seq and scATAC-seq data from PBMCs from 12 COVID-19 individuals at acute infection","dates":{"release":"2025-04-26T00:00:00Z","modification":"2024-01-29T22:17:36.963Z","creation":"2024-01-29T22:17:36.963Z"},"accession":"E-MTAB-13745","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0009809","EFO_0005518","EFO_0003816","EFO_0004184"]}}