Contact:
Nadia Roan, PhD
Gladstone Institutes
University of California, San Francisco
nadia.roan@gladstone.ucsf.edu
nadia.roan@ucsf.edu

Dates of collection: December 2020 to February 2022

Information about the geographic location of data collection: San Francisco Bay Area

Key words: SARS-CoV-2, CyTOF, T cells, pregnant, lactating

Data and file overview:

Included are 348 FCS files from 174 different CyTOF specimens. Each file name begins with a de-identified study participant identifier (ID). The Group category corresponds to whether the participant was non pregnant (Nonpreg), pregnant, or lactating at the time of specimen collection. The Status category indicates whether the sample was obtained prior (Pre) or subsequent (Post) to receiving a 3rd dose of a COVID-19 mRNA vaccine. The Immunity category corresponds to whether at the time of sampling, the participant had only received COVID-19 vaccines (Vac) or whether the participant had received 3 doses of vaccine followed by a breakthrough SARS-CoV-2 infection (Break). The Cell Type category indicates whether data exported correspond to CD4+ or CD8+ T cells. The Cells category indicates whether the cells analyzed were total T cells at baseline (Atlas) or SARS-CoV-2-specific T cells from peptide stimulated samples (SARS2). The Batch category indicates the batch that each specimen was run in. All files were created between March 2022 and
August 2022.

In addition, we include a single Excel (.xlsx) file corresponding to the raw Luminex-derived antibody data from 87 individuals. In the Excel file, each row corresponds to a separate specimen.

• The first column ("ID") corresponds to the de-identified study participant identifier (ID).
• The "Sampling" column indicates the date of specimen collection.
• The "Group" column indicates whether the participant was non-pregnant (Nonpreg), pregnant, or lactating at the time of specimen collection.
• The "Status" column corresponds to whether the specimens were collected before (Pre) or after (Post) receiving the 3rd dose of COVID-19 vaccine. The "Immunity" column indicates whether at the time of sampling, the individual had only received COVID-19 vaccines (Vac), or whether the participant had received 3 doses of vaccine followed by a breakthrough SARS-CoV-2 infection (Break).
• The "IgG anti-N", "IgG anti-RBD", "IgM anti-N", "IgM anti-RBD", "IgA anti-N", and "IgA anti-RBD" columns indicate the corresponding median fluorescence intensity (MFI) values as determined by Luminex, which indicates the relative levels of each of these types of antibodies between the different participants.

Sharing and access information: No licenses or restrictions are placed on the data.

Methodological information: Methods used for generating and analyzing the CyTOF datasets are similar to those described before:

https://elifesciences.org/articles/72619

https://journals.aai.org/jimmunol/article/207/5/1344/234507/Protracted-yet-Coordinated-Differentiation-of-Long

https://doi.org/10.1016/j.celrep.2021.109414

https://doi.org/10.1016/j.xcrm.2020.100081

https://www.nature.com/articles/s41590-023-01724-6

IgG, IgM, and IgA antibodies against the spike receptor binding domain (RBD) or nucleocapsid (N) of the SARS-CoV-2 virus were analyzed with a multiplex-based human serology kit (Bio-Rad, catalog#12014777) according to the manufacturer's instructions. Values shown are in median fluorescence intensity (MFI) as determined by Luminex assay.

Data-specific information: Please see the above information under "data and file overview" and "methodological information".

CyTOF datasets:

ID: Participant identifier
Group: Indicates the physiological state of the participants at the time of sampling
Status: Indicates whether samples were obtained either before or after a 3rd mRNA vaccine dose
Immunity: Indicates whether the participants' immunity were from vaccination only or from breakthrough infection
Cell Type: Indicates whether CD4+ or CD8+ T cells were analyzed
Cells: Indicates whether the data correspond to that of total or SARS-CoV-2-specific T cells
Batch: Indicates the batch in which the specimens were run

Human subjects data

This study was approved by the institutional review board of University of California, San Francisco (UCSF, IRB #20-32077 and IRB #19-29713) and written informed consent was obtained from all study participants, to publish de-identified data in the public domain.