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SARS-CoV-2 Variant Boosters and Breakthrough Infections Drive Functional Differences in the Memory B Cell Repertoire

GSE303324 Homo sapiens (human) RNA-seq (gene expression) 55 samples Submitted 2026/06/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 55 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Samples
55 samples: 45 distinct titles, 7 of them repeatedGroups 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.
Summary (written by the submitters)
Evolving respiratory viruses such as influenza and COVID-19 cause seasonal respiratory illness and death. Updated vaccines with virus variants are made to increase efficacy, but pre-existing immunity affects the response. To understand if variant boosters modify the memory B cell (MBC) repertoire, we analyzed the human MBC response in the COVAIL vaccine trial where individuals previously vaccinated with COVID-19 prototype spike immunogens were boosted with prototype spike, variant spikes, or both.
Read the full summary ↓
We analyzed the cross-reactivity, phenotype and functionality of the MBC response and determined that variant vaccine boosters led to greater recall of cross-reactive MBCs compared to a prototype but limited de novo variant-specific MBC responses. Some study participants also experienced breakthrough infections with SARS-CoV-2 Omicron variants after the vaccine boost that primarily expanded cross-reactive MBCs. These MBCs potently neutralized closely related Omicron virus strains, but displayed less breadth toward more distant Omicron subvariants than MBCs from uninfected individuals. Thus, infection can narrow the cross-reactivity of the memory B cell repertoire.
This dataset
Open GSE303324 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 GSE303324_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1294831 and SRA study SRP602725. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
45 distinct titles, 7 of them repeated
VRC-COVAIL-09-19-2023-VDJ-Pool ×3 VRC-COVAIL-09-20-2023-VDJ-Pool ×3 VRC-COVAIL-09-28-2023-VDJ-Pool ×3 VRC-COVAIL-09-21-2023-VDJ-Pool ×2 VRC-COVAIL-09-26-2023-VDJ-Pool ×2 VRC-COVAIL-09-27-2023-VDJ-Pool ×2 VRC-COVAIL-10-06-2023-VDJ-Pool ×2

How we read this: Read from 55 sample titles: 45 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

+ 15 more — browse all 55 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.