← BioTransfer GEO Dataset Finder
GEO series

CUT&RUN sequencing on wildtype HSCs, MPP3s, GMPs, and macrophages with four weeks M. avium infection

GSE277899 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2025/12/01 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 36 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
36 samples: 12 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
Rare epigenetic alterations are conserved across hematopoietic differentiation stages after mycobacterial infectionJCI insight · 2026
Summary (written by the submitters)
Purpose: Central trained immunity is a phenomenom in which reprogrammed HSPCs differentiate into innate immune cells with heightened immune responses. To determine whether histone modifications are conserved and passed down to downstream lineage cells, we performed CUT&RUN sequencing on various HSPC subpopulations and macrophages in both M. avium infected and naive states. This was done to determine if there were conserved changes across all subpopulations, which would imply to us if specific gene signatures and genomic loci could be conserved for eliciting central trained immunity.
Published in
Rare epigenetic alterations are conserved across hematopoietic differentiation stages after mycobacterial infection
Tran BT, Luna PN, Cao R et al. · JCI insight 2026 · PMID 41364527 · doi:10.1172/jci.insight.193686
This dataset
Open GSE277899 in finder → Find more mouse 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 GSE277899_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 PRJNA1164731 and SRA study SRP534460. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41364527) ↗
Study design
12 conditions, mostly in duplicate
HSC, H3K4me3, infected, biol ×2 MPP3, H3K27ac, naive, biol ×2 MPP3, H3K27ac, infected, biol ×2 MPP3, H3K4me3, infected, biol ×2 GMP, H3K27ac, naive, biol ×2 GMP, H3K4me3, naive, biol ×2 GMP, H3K27ac, infected, biol ×2 GMP, H3K4me3, infected, biol ×2 +16 more

Supports a case/control comparison: 18 samples read as cases, 18 as controls.

How we read this: 12 replicated groups read from 36 sample titles; they account for 24 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

Search all mouse 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.