GEO series

Adipose tissue retains an epigenetic memory of obesity after weight loss [ATAC-seq]

GSE236575 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 22 samples Submitted 2024/11/14 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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: 22 samples: 8 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.
Paper: Adipose tissue retains an epigenetic memory of obesity after weight lossNature · 2024

Summary (written by the submitters)

Reducing body weight to improve metabolic health and related comorbidities is a primary goal in treating obesity. However, maintaining weight loss is a considerable challenge, especially as the body appears to retain an obesogenic memory that defends against body weight changes. Overcoming this barrier for long-term treatment success is difficult because the molecular mechanisms underpinning this phenomenon remain largely unknown.

Read the full summary ↓

Here, by using single-nuclei RNA-sequencing, we show that both human and mouse adipose tissue retain cellular transcriptional changes after appreciable weight loss. Furthermore, we find persistent obesity-induced alterations in the mouse adipocyte epigenome, negatively affecting their function and response to metabolic stimuli. Mice carrying this obesogenic memory show accelerated rebound weight gain, and the epigenetic memory can explain future transcriptional deregulation in adipocytes in response to further high-fat diet feeding. In summary, our findings indicate the existence of an obesogenic memory, largely based on stable epigenetic changes, in mouse adipocytes, and likely other cell types. These changes appear to prime cells for pathological responses in an obesogenic environment, contributing to the problematic "yo-yo" effect often seen with dieting. Targeting these changes in the future could improve long-term weight management and health outcomes.

Published in

Adipose tissue retains an epigenetic memory of obesity after weight loss

Hinte LC, Castellano-Castillo D, Ghosh A et al. · Nature 2024 · PMID 39558077 · doi:10.1038/s41586-024-08165-7

This dataset

Open GSE236575 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 GSE236575_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 PRJNA991593 and SRA study SRP447450. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39558077) ↗

Study design

8 conditions, mostly in triplicate

C_short_ATAC ×3 H_short_ATAC ×3 CC_short_ATAC ×3 HC_short_ATAC ×3 HH_long_ATAC ×3 HHC_long_ATAC ×3 CC_long_ATAC ×2 CCC_long_ATAC ×2

Supports a between-group comparison across 22 samples.

How we read this: 8 replicated groups read from 22 sample titles; they account for 22 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

GSM7558081 C_short_ATAC_1 C_short_ATAC
GSM7558082 H_short_ATAC_1 H_short_ATAC
GSM7558083 CC_short_ATAC_1 CC_short_ATAC
GSM7558085 HC_short_ATAC_1 HC_short_ATAC
GSM7558086 C_short_ATAC_2 C_short_ATAC
GSM7558087 H_short_ATAC_2 H_short_ATAC
GSM7558088 CC_short_ATAC_2 CC_short_ATAC
GSM7558090 HC_short_ATAC_2 HC_short_ATAC
GSM7558091 C_short_ATAC_3 C_short_ATAC
GSM7558092 H_short_ATAC_3 H_short_ATAC
GSM7558093 CC_short_ATAC_3 CC_short_ATAC
GSM7558094 HC_short_ATAC_3 HC_short_ATAC
GSM7558096 CC_long_ATAC_1 CC_long_ATAC
GSM7558097 HH_long_ATAC_1 HH_long_ATAC
GSM7558098 CCC_long_ATAC_1 CCC_long_ATAC
GSM7558099 HHC_long_ATAC_1 HHC_long_ATAC
GSM7558101 CC_long_ATAC_2 CC_long_ATAC
GSM7558102 HH_long_ATAC_2 HH_long_ATAC
GSM7558103 CCC_long_ATAC_2 CCC_long_ATAC
GSM7558104 HHC_long_ATAC_2 HHC_long_ATAC
GSM7558105 HH_long_ATAC_3 HH_long_ATAC
GSM7558107 HHC_long_ATAC_3 HHC_long_ATAC

Datasets on a similar topic

GSE236580 Adipose tissue retains an epigenetic memory of obesity after weight loss 135 samples shares epigenetic, adipose, retains, obesity, memory, weight, loss
GSE236578 Adipose tissue retains an epigenetic memory of obesity after weight loss [TRAP] 20 samples shares epigenetic, adipose, retains, obesity, memory, weight, loss
GSE278003 Single cell RNA sequencing of CD45+ immune cells from tumor and tumor-adjacent mammary adipose tissue in a postmenopausal breast cancer model of lean, obese, and weight loss Trem2+/+ and Trem2-/- mice 92 samples shares adipose, weight, loss
GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares epigenetic, atac-seq, memory
GSE298001 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [ATAC-Seq] 36 samples shares epigenetic, atac-seq
GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares atac-seq, memory
GSE271883 Maternal high-fat diet alters Tet-mediated epigenetic regulation during heart development [ATAC-Seq] 12 samples shares epigenetic, atac-seq
GSE254919 Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy [ATAC-seq] 12 samples shares atac-seq, adipose

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

Share this dataset

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.