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ATR/CHK1/WEE1 dependency in SRSF2-mutated myeloid malignancies

GSE213002 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/11/24 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 5 × SRSF2.P95L.Clone vs 4 × SRSF2.P95R.Clone vs 3 × SRSF2.P95.CloneGroups 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
Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 lossbioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
The aim of this experiment is to characterize mRNA splicing in clones derived from the K562 cell line, which have been genetically engineered using CRISPR/Cas9 to carry SRSF2 mutations frequently observed in myeloid malignancies
Published in
Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss
Eldfors S, Rai S, Sharma V et al. · bioRxiv : the preprint server for biology 2025 · PMID 41279606 · doi:10.1101/2025.10.06.680457
This dataset
Open GSE213002 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 GSE213002_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 PRJNA878761 and SRA study SRP396455. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41279606) ↗
Study design
5 × SRSF2.P95L.Clone vs 4 × SRSF2.P95R.Clone vs 3 × SRSF2.P95.Clone

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 16 sample titles; they account for 12 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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