GEO series

Mutant CEBPA promotes tolerance to inflammatory stress through deficient AP-1 activation [RNA-Seq]

GSE270550 Mus musculus (mouse) RNA-seq (gene expression) 75 samples Submitted 2025/03/11 Platform GPL34290Platform GPL28457Platform GPL34284

At a glance

RNA-seq (gene expression) · mouse · 75 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: 75 samples: 25 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.

Summary (written by the submitters)

The CEBPA transcription factor is frequently mutated in acute myeloid leukemia (AML). Mutations in the CEBPA gene, which are typically biallelic, result in the production of a shorter isoform known as p30. Both the canonical 42-kDa isoform (p42) and the AML-associated p30 isoform bind chromatin and activate transcription, but the specific transcriptional programs controlled by each protein and how they are linked to a selective advantage in AML is not well understood.

Read the full summary ↓

Here, we show that cells expressing the AML-associated p30 have reduced baseline inflammatory gene expression and display altered dynamics of transcriptional induction in response to LPS, consequently impacting cytokine secretion. This confers p30-expressing cells an increased resistance to the adverse effects of prolonged exposure to inflammatory signals. Mechanistically, we show that these differences primarily result from the differential regulation of AP-1 family proteins. In addition, we find that the altered function of the AP-1 member ATF4 in p30-expressing cells alters their response to ER stress. Collectively, these findings uncover a novel link between mutant CEBPA, inflammation and the stress response, potentially revealing a new vulnerability in AML.

This dataset

Open GSE270550 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 GSE270550_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 PRJNA1127485 and SRA study SRP515870. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

25 conditions, mostly in triplicate

Macroph, WT, UT, ×3 Macroph, WT, 2h, ×3 Macroph, WT, 8h, ×3 Macroph, p30, UT, ×3 Macroph, p30, 2h, ×3 Macroph, p30, 8h, ×3 Prog, WT, UT, ×3 Prog, p30, UT, ×3 +17 more

Supports a between-group comparison across 75 samples.

How we read this: 25 replicated groups read from 75 sample titles; they account for 75 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

GSM8346519 Macroph, WT, UT, R1 Macroph, WT, UT,
GSM8346520 Macroph, WT, UT, R2 Macroph, WT, UT,
GSM8346521 Macroph, WT, UT, R3 Macroph, WT, UT,
GSM8346522 Macroph, WT, 2h, R1 Macroph, WT, 2h,
GSM8346523 Macroph, WT, 2h, R2 Macroph, WT, 2h,
GSM8346524 Macroph, WT, 2h, R3 Macroph, WT, 2h,
GSM8346525 Macroph, WT, 8h, R1 Macroph, WT, 8h,
GSM8346526 Macroph, WT, 8h, R2 Macroph, WT, 8h,
GSM8346527 Macroph, WT, 8h, R3 Macroph, WT, 8h,
GSM8346528 Macroph, p30, UT, R1 Macroph, p30, UT,
GSM8346529 Macroph, p30, UT, R2 Macroph, p30, UT,
GSM8346530 Macroph, p30, UT, R3 Macroph, p30, UT,
GSM8346531 Macroph, p30, 2h, R1 Macroph, p30, 2h,
GSM8346532 Macroph, p30, 2h, R2 Macroph, p30, 2h,
GSM8346533 Macroph, p30, 2h, R3 Macroph, p30, 2h,
GSM8346534 Macroph, p30, 8h, R1 Macroph, p30, 8h,
GSM8346535 Macroph, p30, 8h, R2 Macroph, p30, 8h,
GSM8346536 Macroph, p30, 8h, R3 Macroph, p30, 8h,
GSM8346549 Prog, WT, UT, R1 Prog, WT, UT,
GSM8346550 Prog, WT, UT, R2 Prog, WT, UT,
GSM8346551 Prog, WT, UT, R3 Prog, WT, UT,
GSM8346552 Prog, p30, UT, R3 Prog, p30, UT,
GSM8346553 Prog, p30, UT, R1 Prog, p30, UT,
GSM8346554 Prog, p30, UT, R2 Prog, p30, UT,
GSM8346555 Prog, WT, LPS 2h, R1 Prog, WT, LPS 2h,
GSM8346556 Prog, WT, LPS 2h, R2 Prog, WT, LPS 2h,
GSM8346557 Prog, WT, LPS 2h, R3 Prog, WT, LPS 2h,
GSM8346558 Prog, p30, LPS 2h, R3 Prog, p30, LPS 2h,
GSM8346559 Prog, p30, LPS 2h, R1 Prog, p30, LPS 2h,
GSM8346560 Prog, p30, LPS 2h, R2 Prog, p30, LPS 2h,
GSM8346561 HPC-7, p30, UT, R1 HPC-7, p30, UT,
GSM8346562 HPC-7, p30, UT, R2 HPC-7, p30, UT,
GSM8346563 HPC-7, p30, UT, R3 HPC-7, p30, UT,
GSM8346564 HPC-7, p42, UT, R1 HPC-7, p42, UT,
GSM8346565 HPC-7, p42, UT, R2 HPC-7, p42, UT,
GSM8346566 HPC-7, p42, UT, R3 HPC-7, p42, UT,
GSM8346567 HPC-7, EV, UT, R1 HPC-7, EV, UT,
GSM8346568 HPC-7, EV, UT, R2 HPC-7, EV, UT,
GSM8346569 HPC-7, EV, UT, R3 HPC-7, EV, UT,
GSM8346570 HPC-7, p30, LPS 2h, R1 HPC-7, p30, LPS 2h,

+ 35 more — browse all 75 samples with per-sample file links →

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