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Non-classical CD45RBlo memory B-cells are the majority of circulating antigen-specific B-cells following mRNA vaccination and COVID-19 infection.

GSE247488 Homo sapiens (human) Single-cell RNA-seq 15 samples Submitted 2024/05/14 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 15 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
15 samples: 15 samples, each with a distinct title — no replicated groupsGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Atypical and non-classical CD45RB(lo) memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19Nature communications · 2024
Summary (written by the submitters)
Resting memory B-cells can be divided into classical and non-classical groups based on differential expression of markers such as CD27 and CD11c, while activated memory B-cells express a combination of markers, making their ontogeny hard to determine. Here by longitudinal analysis of COVID-19, bacterial sepsis, and BNT162b2 mRNA vaccine recipients by mass cytometry and CITE-seq we describe a three-branch structure of resting B-cell memory consisting of “classical” CD45RB⁺ memory and two branches of CD45RB^lo memory further defined by expression of CD23 and CD11c respectively.
Read the full summary ↓
Stable differences in CD45RB upon activation allowed tracking of activated B-cells and plasmablasts derived from CD45RB⁺ classical and CD45RB^lo non-classical memory B-cells. In both COVID-19 patients and mRNA vaccination, CD45RB^lo B-cells formed the majority of SARS-CoV2 specific memory B-cells while CD45RB⁺ memory was most strongly activated by bacterial Sepsis. These results suggest that diverse non-classical CD45RB^lo memory B-cells consisting of branches of CD11c⁺Tbet⁺ and CD23⁺ fractions form a critical part of responses to viral infection and vaccination.
Published in
Atypical and non-classical CD45RB(lo) memory B cells are the majority of circulating SARS-CoV-2 specific B cells following mRNA vaccination or COVID-19
Priest DG, Ebihara T, Tulyeu J et al. · Nature communications 2024 · PMID 39122676 · doi:10.1038/s41467-024-50997-4
This dataset
Open GSE247488 in finder → Find more human RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE247488_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1038765 and SRA study SRP471264. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39122676) ↗
Study design
15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
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