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Targeting fatty acid metabolism to abrogate differentiation block in pre-leukemia induced by AML1-ETO

GSE270447 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2024/06/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 14 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
14 samples: 4 × LT-HSC cells, Control mouse, vs 4 × GMP cells, Control mouse, vs 3 × LT-HSC cells, AML1/ETO mouse, vs 3 × GMP cells, AML1/ETO mouse,Groups 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
Targeting Fatty Acid Metabolism Abrogates the Differentiation Blockade in Preleukemic CellsCancer research · 2024
Summary (written by the submitters)
To gain the underlying insight into the functional impact of AML1-ETO expressed in HSPCs, RNA-seq was performed on purified LT-HSCs and GMPs from the bone marrow (BM) of both AML1-ETO expressed (AML1/ETO) and Wild-Type (control) C57 mice. Our work suggested that AML1-ETO resulted in impaired hematopoietic reconstitution and increased self-renewal ability.The oxidative phosphorylation and glycolysis decreased significantly in AML1/ETO LT-HSCs accompanied by increased HSC quiescence and reduced cell cycling.
Read the full summary ↓
Furthermore, it was observed that HSCs expressing AML1-ETO exhibited an increased requirement for fatty acids when they differentiated.
Published in
Targeting Fatty Acid Metabolism Abrogates the Differentiation Blockade in Preleukemic Cells
Liu X, Liu Y, Rao Q et al. · Cancer research 2024 · PMID 39264725 · doi:10.1158/0008-5472.CAN-23-3861
This dataset
Open GSE270447 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 GSE270447_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 PRJNA1126647 and SRA study SRP515235. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39264725) ↗
Study design
4 × LT-HSC cells, Control mouse, vs 4 × GMP cells, Control mouse, vs 3 × LT-HSC cells, AML1/ETO mouse, vs 3 × GMP cells, AML1/ETO mouse,

Supports a between-group comparison across 14 samples.

How we read this: 4 replicated groups read from 14 sample titles; they account for 14 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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