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A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture

GSE316956 Homo sapiens (human) RNA-seq (gene expression) 31 samples Submitted 2026/03/13 Platform GPL18573Platform GPL11154
At a glance

RNA-seq (gene expression) · human · 31 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
31 samples: 26 distinct titles, 3 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.
Paper
A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic ArchitecturebioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
This dataset contains the RNA-seq data associated with a CRISPR/Cas9 study for which the screen results (sgRNA reads) are included in the GEO record GSE15547. Specifically, this dataset contains the RNA-seq results used to assess absolute gene expression in Nalm-6 cells, results for 3 PPP3CA knockout polulations, 3 PPP3R1 knockout populations, one FK-506 (tacrolimus) treated population and ERCC spike-in experiments on PABIR1 (formerly FAM122A) knockout cells, each with their own wild type and/or DMSO-treated control samples.
Published in
A Chemical-Genetic Interaction Matrix Reveals Drug Mechanism and Genetic Architecture
Coulombe-Huntington J, Bertomeu T, Huard C et al. · bioRxiv : the preprint server for biology 2026 · PMID 41659671 · doi:10.64898/2026.01.28.701823
This dataset
Open GSE316956 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 GSE316956_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 PRJNA1405595 and SRA study SRP664732. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41659671) ↗
Study design
26 distinct titles, 3 of them repeated
PPP3CA_KO_5D ×3 PPP3R1_KO_5D ×3 TLE4_KO ×2

How we read this: Read from 31 sample titles: 26 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
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.