A single-cell atlas of circulating immune cells over the first two months of age in extremely premature infants

Extremely premature infants (EPI) born prior to 30 weeks gestation are highly susceptible to infection. The trajectory of peripheral immunity in EPIs is poorly understood. Longitudinal analysis of immune cells from 250mL of whole blood at 1 week (n=7), 1 month (n=7), and 2 months (n=5) from 10 EPI was compared to healthy adults (n=6) and to neonatal cord blood (n=13). Single-cell suspensions from individual samples were split to perform single-cell(sc) RNA-, T- and B-cell receptor sequencing (seq), and phosphoprotein mass cytometry. Our scRNAseq data was integrated with existing data from full-term infants at 2 months of age. The trajectory of circulating T-, B-, myeloid, and natural killer cells in EPI infants over the first two months of life is distinct from full-term infants. Peripheral T cell development rapidly progressed over the first month of EPI life with an increase in the proportion of naïve CD4, regulatory, and cycling T cells, accompanied by increased STAT5 signaling compa..., In this study, we performed multi-omic analysis including mass cytometry by time of flight (CyTOF), single-cell RNA sequencing (scRNAseq), T cell and B cell receptor sequencing (TCR and BCR-seq) on circulating immune cells that were isolated from 100 to 250 microliters of blood obtained from extremely premature infants (EPI, n=10) and compared to cord blood from premature (n=5)  and full-term infants (n=5) as well as adult blood. The samples from EPI were obtained at 1 week, 1 month, and 2 months of life. 
Here we have included CyTOF data (.Rdata file format)  that has been gated on live, DNA+, CD45+ circulating leukocytes. Data was demultiplexed using Premessa (https://github.com/ParkerICI/premessa) and automated RPhenograph clustering with k=30 in Cytofkit2 (https://github.com/JinmiaoChenLab/cytofkit2) and included here is the Rdata file that includes analysis of ~15,000 cells that have been clustered based upon surface marker expression to identify 28 distinct populati..., , # **A single-cell atlas of circulating immune cells over the first two months of age in extremely premature infants**

[https://doi.org/10.5061/dryad.pk0p2ngxg](https://doi.org/10.5061/dryad.pk0p2ngxg)

## Description of the data and file structure

Here we have included data from mass cytometry by time of flight (CyTOF) analysis of 15,000 leukocytes from 28 individual samples. Furthermore, there are the major scripts we used for our scRNAseq, TCR, and BCR data analysis. We uploaded 9 files of Python and R scripts. One file is a .Rdata file exported from cytofkit2 of CyTOF data analysis.

1. File: pilotk5.Rdata

Description: Exported data from CyTOF analysis.
2. File: gene-usage.html

Description: R script that was used to determine the BCR gene usage across samples for heavy and light-chain based upon the identified B cell populations in the B cell analysis from the scRNAseq data set.
3. File: All_samples_plots.html. Description: R script that includes all packages used to determ...