COVID-19 vaccination single cell datasets
DOI10.5281/zenodo.8240488Zenodo8240488MaRDI QIDQ6677969FDOQ6677969
Dataset published at Zenodo repository.
Yuhan Hao, Rabi Upadhyay, Ramin S. Herati, Mark J. Mulligan, Bingjie Zhang, John D. Blair, Marie I. Samanovic, Dan R. Littman, Jordan Axelrad, Rahul Satija
Publication date: 25 January 2023
Copyright license: Creative Commons Attribution 4.0 International
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 = "celltypel2", l3 = "celltypel3"), reference.reduction = "spca", reduction.model = "wnn.umap") To use the scATAC-seq data, please run the commands below to update the path of the fragment file for the object. Vaccine_ASAP - readRDS("PBMC_vaccine_ASAP.rds") # remove fragment file information Fragments(Vaccine_ASAP) - NULL # Update the path of the fragment file Fragments(Vaccine_ASAP) - CreateFragmentObject(path = "download/PBMC_vaccine_ASAP_fragments.tsv.gz", cells = Cells(Vaccine_ASAP))
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