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STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

GSE290468 Mus musculus (mouse) Single-cell RNA-seq 169 samples Submitted 2025/06/23 Platform GPL34284Platform GPL33484Platform GPL31217Platform GPL33896Platform GPL33762
At a glance

Single-cell RNA-seq · mouse · 169 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Mus musculus (mouse)
Samples
169 samples: 167 × STAMP vs 2 × Flex_CGroups 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
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imagingCell · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below. PhenoCycler (protein) data is available at https://stjude.app.box.com/s/fg5e5r43heipjh6lchu6m0d612ojwtw1 This is the content within the .tar file: There are 3 STAMPs on the slide i) {PBMC, MCF-7, SK-BR-3}, ii) {MCF-7}, and iii) {SK-BR-3}.You can separate each STAMP by referring to stamp12b_MCF7_new.tsv and stamp12b_SKBR3.tsv - the remaining stamp in the slide will be {PBMC, MCF-7, SK-BR-3}.
Published in
STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging
Pitino E, Pascual-Reguant A, Segato-Dezem F et al. · Cell 2025 · PMID 40532697 · doi:10.1016/j.cell.2025.05.027
This dataset
Open GSE290468 in finder → Find more 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 GSE290468_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 PRJNA1228122 and SRA study SRP597740. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40532697) ↗
Study design
167 × STAMP vs 2 × Flex_C

Supports a between-group comparison across 169 samples.

How we read this: 2 replicated groups read from 169 sample titles; they account for 169 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

+ 129 more — browse all 169 samples with per-sample file links →

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