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Ribo-lite, a method defining paired transcriptome (RNA-seq) and translatome (Ribo-seq) at low input on AML cells from mice treated with 5+3 or vehicle and fed standard amino acids (AA) or branched chain amino acid (BCAA) free diets. [II]

GSE292853 Mus musculus (mouse) RNA-seq (gene expression) 35 samples Submitted 2025/11/18 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 35 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
35 samples: 8 conditions, mostly with about 5 replicates eachGroups 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
OGFOD1 enables AML chemo- and nutrient stress resistance by regulating protein synthesisCell metabolism · 2025
Summary (written by the submitters)
Acute Myeloid Leukemia (AML) commonly relapses after initial chemotherapy response. We assessed metabolic adaptations in chemoresistant cells in vivo before overt relapse, identifying altered branched-chain amino acid (BCAA) levels in patient-derived xenografts (PDX) and immunophenotypically identified leukemia stem cells from AML patients.
Read the full summary ↓
Notably, this was associated with increased BCAA transporter expression with low BCAA catabolism. Restricting of BCAAs further reduced chemoresistant AML cells but relapse still occurred. Among the persisting cells we found an unexpected increase in protein production. This was accompanied by elevated translation of 2-oxoglutarate-and-iron-dependent oxygenase 1 (OGFOD1), a known ribosomal dioxygenase that adjusts the fidelity of tRNA anticodon pairing with coding mRNA1–3 and upregulates protein synthesis in AML driving disease aggressiveness. Inhibiting OGFOD1 impaired translation processing, decreased protein synthesis and improved animal survival even with chemoresistant AML through regulation of protein synthesis. Leukemic cells can therefore persist despite the stress of chemotherapy and nutrient deprivation through adaptive control of translation while sparing normal hematopoiesis. Targeting OGFOD1 may offer a distinctive, translation modifying means of reducing the chemopersisting cells that drive relapse.
Published in
OGFOD1 enables AML chemo- and nutrient stress resistance by regulating protein synthesis
Mayerhofer C, Li D, Kristiansen T et al. · Cell metabolism 2025 · PMID 40961937 · doi:10.1016/j.cmet.2025.08.008
This dataset
Open GSE292853 in finder → Find more mouse 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 GSE292853_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 PRJNA1241746 and SRA study SRP572962. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40961937) ↗
Study design
8 conditions, mostly with about 5 replicates each
Transcriptome BCAA-free plus 5+3 sgScramble A… ×7 Trancriptome BCAA-free plus 5+3 sgOgfod1 AML … ×6 Transcriptome AA vehicle sgScramble AML cells… ×5 Transcriptome AA vehicle sgOgfod1 AML cells b… ×5 Translatome BCAA-free plus 5+3 sgScramble AML… ×4 Translatome AA vehicle sgScramble AML cells b… ×3 Translatome AA vehicle sgOgfdo1 AML cells biol ×3 Translatome BCAA-free plus 5+3 sgOgfod1 AML c… ×2

Supports a between-group comparison across 35 samples.

How we read this: 8 replicated groups read from 35 sample titles; they account for 35 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
Datasets on a similar topic

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