← BioTransfer GEO Dataset Finder
GEO series

A myeloid maturation program initiated by nucleotide depletion during S phase [Cut & Run]

GSE172296 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 47 samples Submitted 2024/05/04 Platform GPL18573Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 47 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
47 samples: 13 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
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stressDevelopmental cell · 2024
Summary (written by the submitters)
Certain cancers, such as acute myeloid leukemia (AML), are caused by malignant stem cells that fail maturation. We sought to mechanistically understand how metabolism might regulate cell fate decisions and to identify metabolic differentiation agents that might be leveraged therapeutically.  We find that nucleotide – purine, pyrimidine, and deoxynucleotide – depletion leads to AML differentiation by way of replication stress.
Read the full summary ↓
Modulation of nucleotide pools leads to transcriptional reprogramming, epigenetic remodeling, and initiation of differentiation which is dependent on the myeloid regulating transcription-factor PU.1. By single-cell RNA sequencing and microscopy, we find that reprogramming downstream of nucleotide depletion occurs as cells undergo replication stress and that the cell fate decision is initiated prior to completion of the cell cycle. Together, these findings suggest that nucleotide metabolism is a critical determinant of hematopoietic progenitor cell fate, clarify the coordination of the fate decision with the cell cycle, and expand upon the class of inhibitors that can be developed or repurposed as novel differentiation therapy.
Published in
Nucleotide depletion promotes cell fate transitions by inducing DNA replication stress
Do BT, Hsu PP, Vermeulen SY et al. · Developmental cell 2024 · PMID 38823395 · doi:10.1016/j.devcel.2024.05.010
This dataset
Open GSE172296 in finder → Find more ChIP / ATAC / CUT&Tag 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 GSE172296_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA722860 and SRA study SRP315285. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38823395) ↗
Study design
13 conditions, mostly in duplicate
63.3_DMSO_H3K4me ×2 63.3_BRQ_H3K4me ×2 ER_cst8644_BRQ ×2 ER_cst8644_E2wd ×2 THP1_H3K27ac_Unt_Unsorted ×2 THP1_H3K27ac_Unt_SortedAll ×2 THP1PIP_H3K27ac_Unt_Early ×2 THP1PIP_H3K27ac_HU100_8h_Early ×2 +26 more

Supports a between-group comparison across 26 samples.

How we read this: 13 replicated groups read from 47 sample titles; they account for 26 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

+ 7 more — browse all 47 samples with per-sample file links →

Datasets on a similar topic

Search all ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.