Global Chromatin Remodeling and Widespread Differential Methylation Changes Underlie Brown Adipose Dysfunction and Dysregulated Metabolism in Response to Chronic Air Pollution Exposure: A Key Role for Reciprocal Regulation by HDAC9 and KDN2b
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 3 × WGBS_FA vs 3 × WGBS_PM vs 3 × ATAC_FA vs 3 × ATAC_PMGroups 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
- Air pollution modulates brown adipose tissue function through epigenetic regulation by HDAC9 and KDM2BJCI insight · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE255961_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1077306 and SRA study SRP490033. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8083500 WGBS_FA1 WGBS_FA
- GSM8083501 WGBS_FA2 WGBS_FA
- GSM8083502 WGBS_FA3 WGBS_FA
- GSM8083503 WGBS_PM1 WGBS_PM
- GSM8083504 WGBS_PM2 WGBS_PM
- GSM8083505 WGBS_PM3 WGBS_PM
- GSM8083506 ATAC_FA1 ATAC_FA
- GSM8083507 ATAC_FA2 ATAC_FA
- GSM8083508 ATAC_FA3 ATAC_FA
- GSM8083509 ATAC_PM1 ATAC_PM
- GSM8083510 ATAC_PM2 ATAC_PM
- GSM8083511 ATAC_PM3 ATAC_PM
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- GSE292357 AMPK signaling is dysregulated in human tendinopathy and loss of AMPKα1 leads to cell, matrix and mechanical dysfunction in mouse Achilles tendon 24 samples shares dysregulated, dysfunction
- GSE249659 Differential CpG methylation at Nnat in the early establishment of beta cell heterogeneity 11 samples shares differential, methylation
- GSE274312 A cis-regulatory element controls HDAC9 expression to fine-tune inflammasome-dependent chronic inflammation 24 samples shares hdac9
- GSE256362 Particle uptake by macrophages triggers bifurcated transcriptional pathways that differentially regulate inflammation and lysosomal gene expression. 157 samples shares differential
- GSE267633 Differential Effects of Prenatal Alcohol Exposure in Mice on Brain Growth and Gene Expression Reveals Early Effects on Cell Cycle and Apoptosis and Delayed Effects on Metabolism in Affected Offspring 151 samples shares differential
- GSE286046 Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells 96 samples shares differential
- GSE252772 Spatial characterization of sex differential regulations in kidney across lifespan 88 samples shares differential
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.