GEO series

A draft map of cis-regulatory sequences in the mouse genome

GSE29184 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 143 samples Submitted 2012/07/01 Platform GPL9250Platform GPL11002Platform GPL13112

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 143 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: 143 samples
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.

Summary (written by the submitters)

The laboratory mouse is the most widely used mammalian model organism in biomedical research. The 2.6 billion bases of the mouse genome share a high degree of conservation with the human genome, so a thorough annotation of the mouse genome will be of significant value to understanding the function of the human genome. To date, most of the functional sequences in the mouse genome have yet to be found, and the cis-regulatory sequences in particular are still poorly annotated.

Read the full summary ↓

Comparative genomics has been a powerful tool for the discovery of these sequences, but it alone cannot resolve their temporal and spatial functions. Recently, ChIP-Seq has been developed to identify cis-regulatory elements in the genomes of several organisms including human, D. melanogaster and C. elegans. We have applied the same experimental approach to a diverse set of 19 tissues and cell types in the mouse, producing a map of nearly 300,000 murine cis-regulatory sequences. This map provides functional annotation to nearly 11% of the mouse genome, and over 70% of conserved, non-coding sequences (CNS). We define tissue-specific enhancers and identify potential transcription factors regulating gene expression in each tissue or cell type. Finally, we demonstrate that much of the mouse genome is organized into domains of coordinately regulated enhancers and promoters. Our results provide a resource for the annotation of functional elements in the mammalian genome and study of mechanisms regulating tissue-specific gene expression. This SuperSeries is composed of the SubSeries listed below.

This dataset

Open GSE29184 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 GSE29184_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 PRJNA139991 and SRA study SRP006786. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22763441) ↗

Samples in this study

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+ 143 more — browse all 143 samples with per-sample file links →

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

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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.