← BioTransfer GEO Dataset Finder
GEO series

Epigenetic evolution of the Ly49 gene family [ATAC-Seq]

GSE226498 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 27 samples Submitted 2024/04/20 Platform GPL20084Platform GPL19057
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 27 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
27 samples: 9 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
Cis-regulatory evolution of the recently expanded Ly49 gene familyNature communications · 2024
Summary (written by the submitters)
Comparative genomics has revealed the rapid lineage-specific expansion of multiple gene families involved in immunity, presumably due to the complexity of ensuring pathogen defense while maintaining self-tolerance. Paralogs within these gene families often evolved distinct roles in immunity. However, less is known about how the epigenome and cis-regulation of these gene families evolved.
Read the full summary ↓
Here we focus on the epigenetic evolution of the rapidly evolving murine Ly49 gene family. Ly49 genes mainly encode either inhibitory or activating surface receptors in natural killer (NK) cells. Together, they fine-tune NK cell activation. We systemically mapped Ly49 transcription initiation, chromatin accessibility, DNA methylation and 3D chromatin interactions. Our data revealed that each Ly49 gene forms a cis-regulatory unit consisted of one or more lowly accessible promoters and a proximal enhancer. Importantly, parallel to the functional divergence of the encoded proteins, inhibitory and activating Ly49 genes have evolved two separate sets of proximal enhancers, likely as a result of lineage-specific losses of enhancer activity. Finally, we show that some Ly49 genes can be cross-regulated by the enhancers of other Ly49 genes, suggesting that the Ly49 family have evolved a concerted regulatory mechanism. Collectively, we demonstrate the different modes of epigenetic evolution for a rapidly expanding gene family essential for host immunity, and provide a rich epigenetic dataset for NK cell research.
Published in
Cis-regulatory evolution of the recently expanded Ly49 gene family
Fan C, Xing X, Murphy SJH et al. · Nature communications 2024 · PMID 38844462 · doi:10.1038/s41467-024-48990-y
This dataset
Open GSE226498 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 GSE226498_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 PRJNA940442 and SRA study SRP425349. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38844462) ↗
Study design
9 conditions, mostly in duplicate
B6_Ly49Dn_ATAC ×3 B6_Ly49Dp_ATAC ×3 B6_Ly49An_ATAC ×2 B6_Ly49Ap_ATAC ×2 B6_Ly49Hn_ATAC ×2 B6_Ly49Hp_ATAC ×2 129_NK_ATAC ×2 NOD_NK_ATAC ×2 +8 more

Supports a between-group comparison across 20 samples.

How we read this: 9 replicated groups read from 27 sample titles; they account for 20 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 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.