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Synthetic antagonist of a histone reader reveals and targets genes essential for inflammation

GSE21910 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 56 samples Submitted 2010/11/10 Platform GPL9250
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 56 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
56 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)
Post-translational modifications of histones determines cell lineage- or signal-specific gene expression. Depending on the type and combination of modifications, histones bind to functionally distinct effector proteins ('readers') that control gene activation or silencing. The current pharmacological modulation of the epigenome aims to control gene expression by regulation of the enzymes that catalyze post-translational histone modifications.
Read the full summary ↓
Here we present a novel pharmacological approach that targets gene expression by interfering with the function of histone ?readers?. We describe the impact of a synthetic compound that selectively occupies the acetylated histone-binding pocket of the Bromodomain and Extra Terminal domain (BET) family of proteins and prevents their interaction with acetylated histones. The bromodomain blocking compound suppresses the expression of a specific subset of key inflammatory genes in activated macrophages and confers protection against LPS-induced septic shock in vivo. Our findings suggest that small molecules specifically targeting histone 'readers' can serve as a new generation of drugs to treat immune diseases.
This dataset
Open GSE21910 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 GSE21910_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 PRJNA126833 and SRA study SRP002485. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 21068722) ↗
Samples in this study

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+ 56 more — browse all 56 samples with per-sample file links →

Datasets on a similar topic

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