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Immunological memory diversity in the human upper airway

GSE270518 Homo sapiens (human) Single-cell RNA-seq 201 samples Submitted 2024/06/24 Platform GPL24676
At a glance

Single-cell RNA-seq · human · 201 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
201 samples: 66 conditions, mostly in duplicateGroups 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
Immunological memory diversity in the human upper airwayNature · 2024
Summary (written by the submitters)
Limited CITE-seq antibody panel and 5' gene expression profiling of human nasopharyngeal cells collected with flocked swabs, paired with TCR and BCR sequencing of NP lymphocytes. FACS-sorted SARS-CoV-2 antigen-specific memory B and T cells with 5' gene expression profiling and scBCR and scTCRseq.
Published in
Immunological memory diversity in the human upper airway
Ramirez SI, Faraji F, Hills LB et al. · Nature 2024 · PMID 39085605 · doi:10.1038/s41586-024-07748-8
This dataset
Open GSE270518 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 GSE270518_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 PRJNA1127438 and SRA study SRP515792. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39085605) ↗
Study design
66 conditions, mostly in duplicate
4041 NP cells, GEX biol ×2 4041 NP cells, CITE-seq biol ×2 4041 NP cells, scTCRseq biol ×2 4041 NP cells, scBCRseq biol ×2 4255 NP cells, GEX biol ×2 4255 NP cells, CITE-seq biol ×2 4255 NP cells, scTCRseq biol ×2 4255 NP cells, scBCRseq biol ×2 +127 more

Supports a between-group comparison across 132 samples.

How we read this: 66 replicated groups read from 201 sample titles; they account for 132 of them. 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

+ 161 more — browse all 201 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.