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Perturbational single-cell RNA sequencing of 104 compounds across six immortalized and four primary cell lines

GSE306429 Homo sapiens (human) Single-cell RNA-seq 348 samples Submitted 2025/10/23 Platform GPL24676Platform GPL21697
At a glance

Single-cell RNA-seq · human · 348 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
348 samples: 348 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
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypesScience (New York, N.Y.) · 2025
Summary (written by the submitters)
we introduce a new perturbational scRNA-seq dataset that includes six immortalized lines (A549, A375, H1AE, HEK293T, HEP2G, and PC3) and four primary lines: CD8+ T-cells (CD8+), CD34+ hematopoietic progenitors (CD34+), primary adipocytes (PAD), and bronchial epithelial cells (HBEC). 104 compounds, including 88 from CMap, were tested across the 10 cell types in duplicate with library-matched controls, resulting in 1,737 scRNA-seq samples comprising a total of 1.26 M cells.
Published in
Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes
DeMeo B, Nesbitt C, Miller SA et al. · Science (New York, N.Y.) 2025 · PMID 41129612 · doi:10.1126/science.adi8577
This dataset
Open GSE306429 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 GSE306429_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 PRJNA1304523 and SRA study SRP608191. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41129612) ↗
Study design
348 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 348 sample titles: 348 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

+ 308 more — browse all 348 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.