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Particle uptake by macrophages triggers bifurcated transcriptional pathways that differentially regulate inflammation and lysosomal gene expression.

GSE256362 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 157 samples Submitted 2024/10/01 Platform GPL21103
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 157 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
157 samples: 61 conditions, mostly in triplicateGroups 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.
Summary (written by the submitters)
Exposure to physical particles is a driver of several inflammatory diseases. Here, we systematically investigated responses of macrophages to pathogenic forms of monosodium urate crystals, calcium pyrophosphate crystals, aluminium salts, and silica nanoparticles. While each particle induced a distinct pattern of gene expression, we also identified a common signature that was preferentially linked to inflammation and acute activation of genes required for lysosomal acidification.
Read the full summary ↓
Using monosodium urate crystals as a model system, we obtained evidence that the program of lysosomal gene expression was regulated by a network of transcription factors that included TFEB and TFE3 and the epigenetic regulators DNMT3A and DOT1L. This lysosomal acidification network operated in parallel with, but largely independently of, a JNK and AP-1 dependent transcription factor network that drove crystal induced chemokine and cytokine gene expression. Mechanistically, the uptake of particles led to early activation of AMPK signalling that was required for activation of TFEB and TFE3 in a process independent of reduced mTOR signalling. These results thereby revealed a mechanism by which the functions of TFEB and TFE3 can be preferentially targeted to specific aspects of lysosomal gene expression, which may provide insights into therapeutic approaches to treat individuals with particle-associated diseases.
This dataset
Open GSE256362 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 GSE256362_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 PRJNA1079273 and SRA study SRP492170. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
61 conditions, mostly in triplicate
Ampka1KO_MSUc ×3 Ampka1KO_PBS ×3 Ampka1WT_MSUc ×3 Ampka1WT_PBS ×3 SGCMSUc ×3 VehicleMSUc ×3 VehiclePBS ×3 DOT1LChIP_MSUc ×3 +57 more

Supports a between-group comparison across 153 samples.

How we read this: 61 replicated groups read from 157 sample titles; they account for 153 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

+ 117 more — browse all 157 samples with per-sample file links →

Datasets on a similar topic

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.