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Epigenetic evolution of the Ly49 gene family

GSE226502 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 65 samples Submitted 2024/04/20 Platform GPL26624Platform GPL20084Platform GPL19057Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 65 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
65 samples: 19 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE226502 in finder → Find more 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 GSE226502_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 PRJNA940439 and SRA study SRP425319. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38844462) ↗
Study design
19 conditions, mostly in duplicate
B6_Ly49Dn_ATAC ×3 B6_Ly49Dp_ATAC ×3 MAP8.B6.Ly49h_KO_Hn_RNA ×2 MAP8.B6.Ly49m_KO_M6_RNA ×2 MAP8.B6.Ly49m_WT_M6_RNA ×2 MAP8.B6.Ly49m_KO_M9_RNA ×2 MAP8.B6.Ly49m_WT_M9_RNA ×2 B6_Ly49An_ATAC ×2 +36 more

Supports a between-group comparison across 40 samples.

How we read this: 19 replicated groups read from 65 sample titles; they account for 40 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

+ 25 more — browse all 65 samples with per-sample file links →

Datasets on a similar topic

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