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Transcription analysis of CBX3::ALK Fusion and EML4-ALK Fusion that drives ALK Activation

GSE311944 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2026/01/13 Platform GPL30172Platform GPL30173
At a glance

RNA-seq (gene expression) · mouse · 18 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
Mus musculus (mouse)
Samples
18 samples: 5 conditions, mostly in triplicateGroups 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
Out-of-frame CBX3::ALK fusion drives ALK activation and therapy responseCell reports. Medicine · 2026
Summary (written by the submitters)
Kinase gene fusions are critical oncogenic drivers and key targets in precision oncology. Here, we report a previously undescribed out-of-frame CBX3::ALK fusion identified in metastatic melanoma. Remarkably, this fusion generates a biologically active ALK protein. In this study, we performed RNA-seq to compare the transcriptional profile of CBX3::ALK with the well-characterized EML4-ALK fusion. Our goal is to evaluate the similarities between these fusions and investigate potential therapeutic targets for CBX3::ALK.
Published in
Out-of-frame CBX3::ALK fusion drives ALK activation and therapy response
Hang JF, Cheng HY, Tsai YS et al. · Cell reports. Medicine 2026 · PMID 41887222 · doi:10.1016/j.xcrm.2026.102697
This dataset
Open GSE311944 in finder → Find more 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 GSE311944_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 PRJNA1371974 and SRA study SRP650218. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41887222) ↗
Study design
5 conditions, mostly in triplicate
ALK expression, biological replicate# ×6 NIH/3T3, EML4-ALK expression, biological repl… ×3 NIH/3T3, GFP control, biological replicate# ×3 MeWo, EML4-ALK expression, biological replica… ×3 MeWo, GFP control, biological replicate# ×3

Supports a between-group comparison across 18 samples.

How we read this: 5 replicated groups read from 18 sample titles; they account for 18 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
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