COVID-19 vaccination single cell datasets
type: Item
instance of: data set
description: The datasets presented here comprise the sequencing data featured in the research paper titled: Multimodal single-cell datasets characterize antigen-specific CD8+T cells across SARS-CoV-2 vaccination and infection: https://www.nature.com/articles/s41590-023-01608-9 Peripheral Blood Mononuclear Cell (PBMC) samples utilized for both CITE-seq and ASAP-seq were systematically collected at four distinct time intervals: Pre-vaccination (Day 0) Post-primary vaccination (Day 2 and Day 10. Seven days post-boost vaccination (Day 28). The count matrix folder containscount matrices for each experimental type, specifically CITE-seq, ASAP-seq, and ECCITE-seq. In addition, we have included the fully integrated, processed Seurat objects for downstream analysis. Details of the content within the count matrix folder are as follows: The RNA, ATAC, and TCR modality outputs were generated using the 10x Cellranger pipeline. HTO and ADT modalities were mapped with Alevin. Outlined below are the three processed single-cell datasets: PBMC_vaccine_CITE.rds: 3 RNA and surface proteins (173 TotalSeq-A antibodies) PBMC_vaccine_ASAP.rds: Chromatin accessibilityand surface proteins(173 TotalSeq-A antibodies) PBMC_vaccine_ECCITE_TCR.rds:5 RNA, surface proteins (137 TotalSeq-C antibodies), TCR and dextramer loaded with peptides of SARS-CoV-2 spike protein. antigen_module_genes.rds: This file contains the vaccine-induced gene sets. antigen_module_peaks.rds: This file contains the DE peaks specific for vaccine-induced cells. To map thescRNA-seq query dataset onto our CITE-seq reference: library(Seurat) PBMC_CITE - readRDS("/zenedo/PBMC_vaccine_CITE.rds") query_scRNA - readRDS("/home/xx/your_own_data.rds") anchors - FindTransferAnchors( reference = PBMC_CITE, query = query_scRNA, normalization.method = "SCT", k.anchor = 5, reference.reduction = "spca", dims = 1:50) query_scRNA - MapQuery( anchorset = anchors, query = query_scRNA, reference = PBMC_CITE, refdata = list( l1 = "celltypel1", l2 = "celltype…
publication date: 2023-01-25T00:00:00Z
author: Bingjie Zhang
author: Rabi Upadhyay
author: Yuhan Hao
author: Marie I. Samanovic
author: Ramin S. Herati
author: John D. Blair
author: Jordan Axelrad
author: Mark J. Mulligan
author: Dan R. Littman
author: Rahul Satija
Zenodo ID: 8240488
DOI: 10.5281/zenodo.8240488
copyright license: Creative Commons Attribution 4.0 International
MaRDI profile type: MaRDI dataset profile
description: Dataset published at Zenodo repository.