COVID-19 vaccination single cell datasets

PBMC samples for CITE-seq and ASAP-seq were collected at four time points: immediately before (Day 0) vaccination, after primary vaccination (Day 2, Day 10), and seven days after boost vaccination (Day 28).

The datasets uploaded here are three processed single-cell datasets:

1. PBMC_vaccine_CITE.rds: 3' RNA and surface proteins (173 TotalSeq-A antibodies)

2. PBMC_vaccine_ASAP.rds: Chromatin accessibility and surface proteins (173 TotalSeq-A antibodies)

3. 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 the scRNA-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))