Hematopoietic Stem Cell Transplant and Healthy Donor Single cell RNA-seq (scRNA-seq) combined with T Cell Receptor (TCR) and B Cell Receptor (BCR) sequencing on Timepoints Surrounding SARS-CoV-2 Vaccination and Infection
Single-cell RNA-seq · human · 48 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Homo sapiens (human)
- Samples
- 48 samples: 48 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
- Impact of memory T cells on SARS-CoV-2 vaccine response in hematopoietic stem cell transplantPloS one · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE266519_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1107496 and SRA study SRP505611. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 30 samples read as cases, 18 as controls.
How we read this: Read from 48 sample titles: 48 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.
- GSM8248767 Patient P7, pbmc_01, Pre-Vaccination, scRNAseq
- GSM8248768 Patient P7, pbmc_01, Pre-Vaccination, BCR sequencing
- GSM8248769 Patient P7, pbmc_01, Pre-Vaccination, TCR sequencing
- GSM8248770 Patient P7, pbmc_02, Post-Vaccination, scRNAseq
- GSM8248771 Patient P7, pbmc_02, Post-Vaccination, BCR seqeuncing
- GSM8248772 Patient P7, pbmc_02, Post-Vaccination, TCR seqeuncing
- GSM8248773 Patient P19, pbmc_03, Pre-Vaccination, scRNAseq
- GSM8248774 Patient P19, pbmc_03, Pre-Vaccination, BCR
- GSM8248775 Patient P19, pbmc_03, Pre-Vaccination, TCR
- GSM8248776 Patient P19, pbmc_04, Post-Vaccination, scRNAseq
- GSM8248777 Patient P19, pbmc_04, Post-Vaccination, BCR
- GSM8248778 Patient P19, pbmc_04, Post-Vaccination, TCR
- GSM8248779 Patient P28, pbmc_05, Pre-Vaccination, scRNAseq
- GSM8248780 Patient P28, pbmc_05, Pre-Vaccination, BCR
- GSM8248781 Patient P28, pbmc_05, Pre-Vaccination, TCR
- GSM8248782 Patient P28, pbmc_06, Post-Vaccination, scRNAseq
- GSM8248783 Patient P28, pbmc_06, Post-Vaccination, BCR
- GSM8248784 Patient P28, pbmc_06, Post-Vaccination, TCR
- GSM8248785 Patient P28, pbmc_07, Post-Infection, scRNAseq
- GSM8248786 Patient P28, pbmc_07, Post-Infection, BCR
- GSM8248787 Patient P28, pbmc_07, Post-Infection, TCR
- GSM8248788 Healthy Control 01, pbmc_08, Post-Vaccination, scRNAseq
- GSM8248789 Healthy Control 01, pbmc_08, Post-Vaccination, BCR
- GSM8248790 Healthy Control 01, pbmc_08, Post-Vaccination, TCR
- GSM8248791 Patient P27, pbmc_09, Pre-Vaccination, scRNAseq
- GSM8248792 Patient P27, pbmc_09, Pre-Vaccination, BCR
- GSM8248793 Patient P27, pbmc_09, Pre-Vaccination, TCR
- GSM8248794 Patient P27, pbmc_10, Post-Vaccination, scRNAseq
- GSM8248795 Patient P27, pbmc_10, Post-Vaccination, BCR
- GSM8248796 Patient P27, pbmc_10, Post-Vaccination, TCR
- GSM8248797 Patient P27, pbmc_11, Post-Infection, scRNAseq
- GSM8248798 Patient P27, pbmc_11, Post-Infection, BCR
- GSM8248799 Patient P27, pbmc_11, Post-Infection, TCR
- GSM8248800 Healthy Control 01, pbmc_12, Pre-Vaccination, scRNAseq
- GSM8248801 Healthy Control 01, pbmc_12, Pre-Vaccination, BCR
- GSM8248802 Healthy Control 01, pbmc_12, Pre-Vaccination, TCR
- GSM8248803 Healthy Control 02, pbmc_13, Pre-Vaccination, scRNAseq
- GSM8248804 Healthy Control 02, pbmc_13, Pre-Vaccination, BCR
- GSM8248805 Healthy Control 02, pbmc_13, Pre-Vaccination, TCR
- GSM8248806 Healthy Control 03, pbmc_14, Post-Vaccination, scRNAseq
+ 8 more — browse all 48 samples with per-sample file links →
- GSE288562 Multi-Omics Analysis of the Immunological State at Baseline and Following SARS-CoV-2 mRNA Vaccination in Lung Transplant Recipients 14 samples shares sars-cov-2, vaccination, transplant
- GSE288346 Multi-Omics Analysis of the Immunological State at Baseline and Following SARS-CoV-2 mRNA Vaccination in Lung Transplant Recipients [RNA-seq] 106 samples shares sars-cov-2, vaccination, transplant
- GSE210231 CD8+ T cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by shifts in clonal dominance 931 samples shares sars-cov-2, vaccination
- GSE260763 Expansion of memory Vδ2 T cells following SARS-CoV-2 vaccination revealed by temporal single-cell transcriptomics 60 samples shares sars-cov-2, vaccination
- GSE244297 Memory B cells dominate the early antibody-secreting cell response to SARS-CoV-2 mRNA vaccination in naïve individuals independently of their antibody affinity 24 samples shares sars-cov-2, vaccination
- GSE289648 Maternal acute SARS-CoV-2 infection impairs preimplantation embryo development and reprograms early offspring hematopoietic system 102 samples shares sars-cov-2, hematopoietic
- GSE250025 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 84 samples shares sars-cov-2, vaccination
- GSE250023 Impaired innate and adaptive immune responses to BNT162b2 SARS-CoV-2 vaccination in systemic lupus erythematosus 75 samples shares sars-cov-2, vaccination
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.