GEO series

Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation [scRNA-seq]

GSE286398 Mus musculus (mouse) Single-cell RNA-seq 13 samples Submitted 2025/08/12 Platform GPL21103

At a glance

Single-cell RNA-seq · mouse · 13 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 13 samples: 6 conditions, mostly in duplicateGroups 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: Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiationCell death & disease · 2025

Summary (written by the submitters)

The lysine-specific demethylase 1 (LSD1) regulates hematopoietic stem cell differentiation and has been identified as a therapeutic target in hematological disorders. LSD1 demethylates mono and dimethylated histones 3 at lysine 4 and 9. In addition, it acts as a scaffold for the formation of chromatin-modifying complexes that regulates the transcription of myeloid-lineage-specific genes in complex with GFI1, a transcriptional repressor.

Read the full summary ↓

While both enzymatic and non-enzymatic functions of LSD1 have been well defined, the relative importance of these two functions in hematopoiesis remains incompletely understood. Here, we investigated the contribution of enzymatic and non-enzymatic functions of LSD1 to myelopoiesis. We show that myeloid differentiation is independent of the enzymatic functions of LSD1 but requires the non-enzymatic, scaffolding function, which directs GFI1 binding to target sequences. In absence of the LSD1 protein, GFI1 DNA binding is diminished and myeloid cell differentiation arrests at an immature, myelomonocytic-like cell stage, which overexpresses Prtn3. We provide functional data implicating Prtn3 as an effector of the stem cell expansion and myeloid maturation block caused by the loss of LSD1.

Published in

Lysine-specific demethylase 1 regulates hematopoietic stem cell expansion and myeloid cell differentiation

Staehle HF, Koellerer C, Staehle AM et al. · Cell death & disease 2025 · PMID 40813574 · doi:10.1038/s41419-025-07951-z

This dataset

Open GSE286398 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 GSE286398_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1209073 and SRA study SRP556541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40813574) ↗

Study design

6 conditions, mostly in duplicate

Whole BM, ei ctrl, Mouse ×3 Whole BM, ko ctrl, Mouse ×2 Whole BM, ko, Mouse ×2 Whole BM, ko ctrl BMT, Mouse ×2 Whole BM, ko BMT, Mouse ×2 Whole BM, ei, Mouse ×2

Supports a between-group comparison across 13 samples.

How we read this: 6 replicated groups read from 13 sample titles; they account for 13 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

GSM8726418 Whole BM, ko ctrl, Mouse 1 Whole BM, ko ctrl, Mouse
GSM8726419 Whole BM, ko, Mouse 1 Whole BM, ko, Mouse
GSM8726420 Whole BM, ko ctrl, Mouse 2 Whole BM, ko ctrl, Mouse
GSM8726421 Whole BM, ko, Mouse 2 Whole BM, ko, Mouse
GSM8726422 Whole BM, ko ctrl BMT, Mouse 1 Whole BM, ko ctrl BMT, …
GSM8726423 Whole BM, ko ctrl BMT, Mouse 2 Whole BM, ko ctrl BMT, …
GSM8726424 Whole BM, ko BMT, Mouse 1 Whole BM, ko BMT, Mouse
GSM8726425 Whole BM, ko BMT, Mouse 2 Whole BM, ko BMT, Mouse
GSM8726426 Whole BM, ei ctrl, Mouse 1 Whole BM, ei ctrl, Mouse
GSM8726427 Whole BM, ei ctrl, Mouse 2 Whole BM, ei ctrl, Mouse
GSM8726428 Whole BM, ei, Mouse 1 Whole BM, ei, Mouse
GSM8726429 Whole BM, ei, Mouse 2 Whole BM, ei, Mouse
GSM8795005 Whole BM, ei ctrl, Mouse 3 Whole BM, ei ctrl, Mouse

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