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BRG1 contributes to the global chromatin accessibility revealed by its acute depletion

GSE156569 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 102 samples Submitted 2024/03/05 Platform GPL21493
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 102 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
102 samples: 25 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
Acute depletion of BRG1 reveals its primary function as an activator of transcriptionNature communications · 2024
Summary (written by the submitters)
DNase I hypersensitivity (DHS) of chromatin indicates the presence of important regulatory elements of transcription such as enhancers and promoters and plays critical roles for their activities. However, the mechanisms that control the global DHS have not been fully understood.
Read the full summary ↓
In this report, we show that acute depletion of BRG1 by the auxin-dependent degron system, the essential ATPase subunit of the mammalian chromatin remodeling SWI/SNF-like BAF complexes, severely compromised genome-wide DHSs of chromatin, while the traditional conditional deletion of the Brg1 gene using Cre/Flox system led to only very modest changes of DHSs. The global decrease of DHSs is associated with a genome-wide decrease of transcription. We demonstrate that the DHS change is related with changes in nucleosome positioning at promoters and enhancers. Our data suggest that acute depletion of proteins reveal target genes of BRG1 that are not detected by the traditional models.
Published in
Acute depletion of BRG1 reveals its primary function as an activator of transcription
Ren G, Ku WL, Ge G et al. · Nature communications 2024 · PMID 38811575 · doi:10.1038/s41467-024-48911-z
This dataset
Open GSE156569 in finder → Find more mouse 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 GSE156569_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 PRJNA658358 and SRA study SRP278243. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38811575) ↗
Study design
25 conditions, mostly in duplicate
6000 ×4 DNAse_WT 10K T cell GFP+ 10hr, with 293T ×3 DNAse_KO Brg1-AID 10K T cell GFP+ 10hr, with … ×3 DNAse_NC Brg1f/f Th1 Day6 WT ×3 DNAse_NC Brg1f/f Th1 Day6 KO ×3 DNAse_NC Brgf/f mice hepatocytes Dnase #4 WT ×3 ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs Brg1 ×2 ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs Brg1 ×2 +62 more

Supports a between-group comparison across 57 samples.

How we read this: 25 replicated groups read from 102 sample titles; they account for 57 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

+ 62 more — browse all 102 samples with per-sample file links →

Datasets on a similar topic

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